9NPC | pdb_00009npc

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group I212121 at 2.65 A

PDB DOI: https://doi.org/10.2210/pdb9NPC/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-11 Released: 2025-11-12
Deposition Author(s): Martins, M.P., Spadeto, J.P.M., Miyamoto, R.Y., Morais, M.A.B., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group I212121 at 2.65 A

Martins, M.P., Spadeto, J.P.M., Miyamoto, R.Y., Morais, M.A.B., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 278.55 kDa
Atom Count: 18,386
Modeled Residue Count: 2,210
Deposited Residue Count: 2,394
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 2	A, B, C	798	metagenome	Mutation(s): 0 EC: 3.2.1.25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C]	AA [auth C], M [auth A], U [auth B], V [auth B], Z [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain J [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] R [auth B] I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], Y [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain O [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], W [auth C], X [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.853	α = 90
b = 192.001	β = 90
c = 191.921	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/04891-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/09793-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/06298-0