3K3C | pdb_00003k3c

The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62

PDB DOI: https://doi.org/10.2210/pdb3K3C/pdb

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

Deposited: 2009-10-02 Released: 2010-09-29
Deposition Author(s): King-Scott, J., Tucker, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.212 (Depositor), 0.211 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62

King-Scott, J., Tucker, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 73.81 kDa
Atom Count: 5,976
Modeled Residue Count: 604
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Rv1364c/MT1410	A, B, C, D	158	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT1410, MTCY02B10.28c, Rv1364c EC: 2.7.11.1 (UniProt), 3.1.3.16 (UniProt)
UniProt
Find proteins for P9WLZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WLZ7 Go to UniProtKB: P9WLZ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WLZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	F [auth A] M [auth B] S [auth C] T [auth C] U [auth D] F [auth A], M [auth B], S [auth C], T [auth C], U [auth D], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth D]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.212 (Depositor), 0.211 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.069	α = 90
b = 63.823	β = 89.95
c = 61.305	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
Auto-Rickshaw	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

King-Scott, J.

Tucker, P.A.

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Refinement description