1YK3

Crystal structure of Rv1347c from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb1YK3/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-01-16 Released: 2005-02-01
Deposition Author(s): Card, G.L., Peterson, N.A., Smith, C.A., Rupp, B., Schick, B.M., Baker, E.N., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258
R-Value Work: 0.227
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 191.52 kDa
Atom Count: 13,515
Modelled Residue Count: 1,586
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Rv1347c/MT1389	A, B, C, D, E A, B, C, D, E, F, G, H	210	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: Rv1347c
UniProt
Find proteins for P9WK15 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK15 Go to UniProtKB: P9WK15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth E] SDF format, chain K [auth G] MOL2 format, chain I [auth D] MOL2 format, chain J [auth E] MOL2 format, chain K [auth G]	I [auth D], J [auth E], K [auth G]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth G] Interactions & Density Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258
R-Value Work: 0.227
R-Value Observed: 0.227
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.665	α = 90
b = 77.261	β = 90
c = 296.514	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Structure summary

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Help and Resources

1YK3

Crystal structure of Rv1347c from Mycobacterium tuberculosis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)