3NQI | pdb_00003nqi

Crystal structure of a Putative lipoprotein (BF3042) from Bacteroides fragilis NCTC 9343 at 1.87 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NQI/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-29 Released: 2010-08-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.191 (Depositor), 0.195 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Putative lipoprotein (BF3042) from Bacteroides fragilis NCTC 9343 at 1.87 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 112.78 kDa
Atom Count: 7,821
Modeled Residue Count: 922
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein	A, B, C, D	246	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF3042
UniProt
Find proteins for A0A380YR22 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore A0A380YR22 Go to UniProtKB: A0A380YR22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A380YR22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth D] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth D] SDF format, chain Q [auth B] SDF format, chain PA [auth D] SDF format, chain P [auth B] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] GA [auth C] H [auth A] E [auth A], F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], IA [auth C], JA [auth C], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], W [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain UA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] L [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], L [auth A], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], UA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain UA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain UA [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain OA [auth C] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain OA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B], FA [auth B], OA [auth C], VA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain OA [auth C] Focus chain VA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain OA [auth C] Focus chain VA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain TA [auth D] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	I [auth A] J [auth A] K [auth A] KA [auth C] LA [auth C] I [auth A], J [auth A], K [auth A], KA [auth C], LA [auth C], TA [auth D], X [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain TA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain TA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.220 (Depositor), 0.224 (DCC)
R-Value Work: 0.191 (Depositor), 0.195 (DCC)
R-Value Observed: 0.192 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.49	α = 90
b = 77.227	β = 103.85
c = 97.406	γ = 90

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
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, Refinement description, Structure summary