3SB4 | pdb_00003sb4

Crystal structure of a leucine-rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution

PDB DOI: https://doi.org/10.2210/pdb3SB4/pdb

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

Deposited: 2011-06-03 Released: 2011-06-22
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical leucine rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 75.31 kDa
Atom Count: 5,738
Modeled Residue Count: 657
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical leucine rich repeat protein	A, B	329	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_1240
UniProt
Find proteins for Q8A8C7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A8C7 Go to UniProtKB: Q8A8C7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A8C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] 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 L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] 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 L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.170 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.21	α = 109.8
b = 62.13	β = 93.75
c = 66.86	γ = 91.05

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-11-23
Changes: Structure summary
Version 1.3: 2014-12-24
Changes: Structure summary
Version 1.4: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.5: 2023-02-01
Changes: Database references, Derived calculations
Version 1.6: 2024-11-06
Changes: Data collection, Structure summary

3SB4 | pdb_00003sb4

Crystal structure of a leucine-rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution

Literature

Crystal structure of a Hypothetical leucine rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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