3HTN | pdb_00003htn

Crystal structure of a putative dna binding protein (bt_1116) from bacteroides thetaiotaomicron vpi-5482 at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HTN/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-12 Released: 2009-06-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.167 (Depositor), 0.170 (DCC)
R-Value Work:
0.143 (Depositor), 0.150 (DCC)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Putative DNA binding protein (NP_810029.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 52.77 kDa
Atom Count: 4,286
Modeled Residue Count: 425
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA binding protein	A, B, C	149	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_1116, NP_810029.1
UniProt
Find proteins for Q8A8Q1 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A8Q1 Go to UniProtKB: Q8A8Q1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A8Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], O [auth B], R [auth C], S [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] L [auth B] M [auth B] E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.167 (Depositor), 0.170 (DCC)
R-Value Work: 0.143 (Depositor), 0.150 (DCC)
R-Value Observed: 0.145 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33HTN

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 90.688	β = 90
c = 53.888	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary