4PZU | pdb_00004pzu

Crystal structure of a putative uncharacterize protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb4PZU/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-31 Released: 2014-04-23
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative uncharacterize protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis

Edwards, T.E., Dranow, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 232.88 kDa
Atom Count: 15,706
Modeled Residue Count: 1,867
Deposited Residue Count: 2,048
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv3404c/MT3512	A, B, C, D, E A, B, C, D, E, F, G, H	256	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT3412, MT3512, MTCY78.24, Rv3404c EC: 2.1.2
UniProt
Find proteins for P9WKZ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKZ3 Go to UniProtKB: P9WKZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WKZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth G] CA [auth G] DA [auth H] I [auth A] AA [auth F], BA [auth G], CA [auth G], DA [auth H], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth D], V [auth E], W [auth E], X [auth E], Y [auth F], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34PZU

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.08	α = 90
b = 136.45	β = 103.74
c = 99.97	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-10-22
Changes: Structure summary