3QWN | pdb_00003qwn

Crystal structure of a NigD-like immunity protein (BACCAC_03262) from Bacteroides caccae ATCC 43185 at 2.42 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QWN/pdb

Classification: ANTITOXIN
Organism(s): Bacteroides caccae ATCC 43185
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-28 Released: 2011-03-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Hypothetical nigD-like protein (BACCAC_03262) from Bacteroides caccae at 2.42 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 289.45 kDa
Atom Count: 20,253
Modeled Residue Count: 2,463
Deposited Residue Count: 2,568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical nigD-like protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	214	Bacteroides caccae ATCC 43185	Mutation(s): 0 Gene Names: BACCAC_03262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DB [auth L] SDF format, chain UA [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain DB [auth L] MOL2 format, chain UA [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain DB [auth L] mmCIF format, chain UA [auth I]	CA [auth D], DB [auth L], UA [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DB [auth L] Focus chain UA [auth I] Interactions & Density Focus chain CA [auth D] Focus chain DB [auth L] Focus chain UA [auth I]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth K] SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain CB [auth L] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain S [auth B] SDF format, chain SA [auth I] SDF format, chain T [auth B] SDF format, chain TA [auth I] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth J] SDF format, chain W [auth D] SDF format, chain WA [auth J] SDF format, chain X [auth D] SDF format, chain XA [auth J] SDF format, chain Y [auth D] SDF format, chain YA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain CB [auth L] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth K] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth L] mmCIF format, chain CB [auth L] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth I] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth J] mmCIF format, chain W [auth D] mmCIF format, chain WA [auth J] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth J] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth K] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth K]	AA [auth D] AB [auth K] BA [auth D] BB [auth L] CB [auth L] AA [auth D], AB [auth K], BA [auth D], BB [auth L], CB [auth L], DA [auth E], EA [auth E], FA [auth E], GA [auth E], HA [auth E], IA [auth F], JA [auth F], KA [auth G], LA [auth G], M [auth A], MA [auth G], N [auth A], NA [auth G], O [auth A], OA [auth G], P [auth A], PA [auth H], Q [auth B], QA [auth H], R [auth B], RA [auth I], S [auth B], SA [auth I], T [auth B], TA [auth I], U [auth C], V [auth C], VA [auth J], W [auth D], WA [auth J], X [auth D], XA [auth J], Y [auth D], YA [auth K], Z [auth D], ZA [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth D] Focus chain WA [auth J] Focus chain X [auth D] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth D] Focus chain WA [auth J] Focus chain X [auth D] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33QWN

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.31	α = 90
b = 132.31	β = 90
c = 163.35	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-12-24
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary