8YEB | pdb_00008yeb

Crystal structure of L-ribulose 3-epimerase from Arthrobacter globiformis M30

PDB DOI: https://doi.org/10.2210/pdb8YEB/pdb

Classification: ISOMERASE
Organism(s): Arthrobacter globiformis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-02-12
Deposition Author(s): Watanabe, M., Nakamich, Y., Mine, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.243 (DCC)
R-Value Work:
0.201 (Depositor), 0.207 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of L-ribulose 3-epimerase from Arthrobacter globiformis M30

Watanabe, M., Nakamich, Y., Mine, S.

To be published.

Macromolecule Content

Total Structure Weight: 517.99 kDa
Atom Count: 36,664
Modeled Residue Count: 4,623
Deposited Residue Count: 4,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketose 3-epimerase	A B [auth E] C [auth B] D [auth C] E [auth D] A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H, I, J, K, L, M, N, O, P	297	Arthrobacter globiformis	Mutation(s): 0 Gene Names: DAE EC: 5.1.3
UniProt
Find proteins for A0A1L7NQ96 (Arthrobacter globiformis) Explore A0A1L7NQ96 Go to UniProtKB: A0A1L7NQ96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L7NQ96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain S [auth E] SDF format, chain V [auth C] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain S [auth E] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain S [auth E] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth F]	AA [auth G], S [auth E], V [auth C], Y [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain S [auth E] Focus chain V [auth C] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain S [auth E] Focus chain V [auth C] Focus chain Y [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain IA [auth O] SDF format, chain JA [auth P] SDF format, chain Q [auth A] SDF format, chain R [auth E] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth F] SDF format, chain Z [auth G] SDF format, chain HA [auth N] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth E] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain HA [auth N] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth E] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain HA [auth N]	BA [auth H] CA [auth I] DA [auth J] EA [auth K] FA [auth L] BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], Q [auth A], R [auth E], T [auth B], U [auth C], W [auth D], X [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain Q [auth A] Focus chain R [auth E] Focus chain T [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain Q [auth A] Focus chain R [auth E] Focus chain T [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth F] Focus chain Z [auth G]