3CIS | pdb_00003cis

The Crystal Structure of Rv2623 from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb3CIS/pdb

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

Deposited: 2008-03-11 Released: 2009-03-17
Deposition Author(s): Bilder, P., Drumm, J., Mi, K., Chan, J., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.268 (Depositor), 0.250 (DCC)
R-Value Work:
0.250 (Depositor), 0.250 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The Crystal Structure of Rv2623 : a Novel, Tandem-Repeat Universal Stress Protein of Mycobacterium tuberculosis

Drumm, J., Mi, K., Bilder, P., Almo, S.C., Chan, J.

To be published.

Macromolecule Content

Total Structure Weight: 273.23 kDa
Atom Count: 18,138
Modeled Residue Count: 2,300
Deposited Residue Count: 2,472
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	A, B, C, D, E A, B, C, D, E, F, G, H	309	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: TB31.7
UniProt
Find proteins for P9WFD7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFD7 Go to UniProtKB: P9WFD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth G] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] EA [auth F] FA [auth F] IA [auth G] AA [auth E], BA [auth E], EA [auth F], FA [auth F], IA [auth G], JA [auth G], K [auth A], L [auth A], MA [auth H], NA [auth H], O [auth B], P [auth B], S [auth C], T [auth C], W [auth D], X [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	CA [auth F] DA [auth F] GA [auth G] HA [auth G] I [auth A] CA [auth F], DA [auth F], GA [auth G], HA [auth G], I [auth A], J [auth A], KA [auth H], LA [auth H], M [auth B], N [auth B], Q [auth C], R [auth C], U [auth D], V [auth D], Y [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.268 (Depositor), 0.250 (DCC)
R-Value Work: 0.250 (Depositor), 0.250 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.975	α = 90
b = 241.48	β = 90
c = 241.659	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2020-07-29
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Refinement description