3HTY

Crystal structure of a lipocalin-like protein (BT_0869) from Bacteroides thetaiotaomicron VPI-5482 at 1.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HTY/pdb

Classification: structural genomics, unknown function
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-12 Released: 2009-07-07
Deposition Author(s): Joint Center for Structural Genomics, Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 (NP_809782.1) at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 170.73 kDa
Atom Count: 13,220
Modelled Residue Count: 1,493
Deposited Residue Count: 1,504
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 protein BT_0869	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	94	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_0869, NP_809782.1
UniProt
Find proteins for Q8A9E6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A9E6 Go to UniProtKB: Q8A9E6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A9E6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain OA [auth H] SDF format, chain SA [auth I] SDF format, chain AA [auth D] SDF format, chain BB [auth K] SDF format, chain CB [auth K] SDF format, chain DB [auth K] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GB [auth L] SDF format, chain LA [auth G] SDF format, chain LB [auth N] SDF format, chain MB [auth N] SDF format, chain NA [auth H] SDF format, chain QB [auth O] SDF format, chain RB [auth O] SDF format, chain TA [auth I] SDF format, chain V [auth C] SDF format, chain VB [auth P] SDF format, chain WA [auth J] MOL2 format, chain OA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain AA [auth D] MOL2 format, chain BB [auth K] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth K] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain LA [auth G] MOL2 format, chain LB [auth N] MOL2 format, chain MB [auth N] MOL2 format, chain NA [auth H] MOL2 format, chain QB [auth O] MOL2 format, chain RB [auth O] MOL2 format, chain TA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain VB [auth P] MOL2 format, chain WA [auth J]	AA [auth D] BB [auth K] CB [auth K] DB [auth K] EA [auth F] AA [auth D], BB [auth K], CB [auth K], DB [auth K], EA [auth F], FA [auth F], GB [auth L], LA [auth G], LB [auth N], MB [auth N], NA [auth H], OA [auth H], QB [auth O], RB [auth O], SA [auth I], TA [auth I], V [auth C], VB [auth P], WA [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BB [auth K] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GB [auth L] Focus chain LA [auth G] Focus chain LB [auth N] Focus chain MB [auth N] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain QB [auth O] Focus chain RB [auth O] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain V [auth C] Focus chain VB [auth P] Focus chain WA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain BB [auth K] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GB [auth L] Focus chain LA [auth G] Focus chain LB [auth N] Focus chain MB [auth N] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain QB [auth O] Focus chain RB [auth O] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain V [auth C] Focus chain VB [auth P] Focus chain WA [auth J]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain CA [auth E] SDF format, chain EB [auth K] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IB [auth L] SDF format, chain MA [auth G] SDF format, chain PB [auth N] SDF format, chain Q [auth A] SDF format, chain RA [auth H] SDF format, chain UA [auth I] SDF format, chain UB [auth O] SDF format, chain VA [auth I] SDF format, chain W [auth C] SDF format, chain WB [auth P] SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain FB [auth K] SDF format, chain HB [auth L] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain JB [auth M] SDF format, chain KA [auth F] SDF format, chain KB [auth M] SDF format, chain NB [auth N] SDF format, chain OB [auth N] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain R [auth A] SDF format, chain S [auth B] SDF format, chain SB [auth O] SDF format, chain T [auth B] SDF format, chain TB [auth O] SDF format, chain U [auth B] SDF format, chain X [auth C] SDF format, chain XA [auth J] SDF format, chain Y [auth C] SDF format, chain YA [auth J] SDF format, chain Z [auth C] SDF format, chain ZA [auth J] MOL2 format, chain AB [auth J] MOL2 format, chain CA [auth E] MOL2 format, chain EB [auth K] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IB [auth L] MOL2 format, chain MA [auth G] MOL2 format, chain PB [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain UB [auth O] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain WB [auth P] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain FB [auth K] MOL2 format, chain HB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain JB [auth M] MOL2 format, chain KA [auth F] MOL2 format, chain KB [auth M] MOL2 format, chain NB [auth N] MOL2 format, chain OB [auth N] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth O] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth O] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth J]	AB [auth J] BA [auth D] CA [auth E] DA [auth E] EB [auth K] AB [auth J], BA [auth D], CA [auth E], DA [auth E], EB [auth K], FB [auth K], GA [auth F], HA [auth F], HB [auth L], IA [auth F], IB [auth L], JA [auth F], JB [auth M], KA [auth F], KB [auth M], MA [auth G], NB [auth N], OB [auth N], PA [auth H], PB [auth N], Q [auth A], QA [auth H], R [auth A], RA [auth H], S [auth B], SB [auth O], T [auth B], TB [auth O], U [auth B], UA [auth I], UB [auth O], VA [auth I], W [auth C], WB [auth P], X [auth C], XA [auth J], Y [auth C], YA [auth J], Z [auth C], ZA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth K] Focus chain FB [auth K] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain JB [auth M] Focus chain KA [auth F] Focus chain KB [auth M] Focus chain MA [auth G] Focus chain NB [auth N] Focus chain OB [auth N] Focus chain PA [auth H] Focus chain PB [auth N] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth B] Focus chain SB [auth O] Focus chain T [auth B] Focus chain TB [auth O] Focus chain U [auth B] Focus chain UA [auth I] Focus chain UB [auth O] Focus chain VA [auth I] Focus chain W [auth C] Focus chain WB [auth P] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain YA [auth J] Focus chain Z [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth K] Focus chain FB [auth K] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain JB [auth M] Focus chain KA [auth F] Focus chain KB [auth M] Focus chain MA [auth G] Focus chain NB [auth N] Focus chain OB [auth N] Focus chain PA [auth H] Focus chain PB [auth N] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth B] Focus chain SB [auth O] Focus chain T [auth B] Focus chain TB [auth O] Focus chain U [auth B] Focus chain UA [auth I] Focus chain UB [auth O] Focus chain VA [auth I] Focus chain W [auth C] Focus chain WB [auth P] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain YA [auth J] Focus chain Z [auth C] Focus chain ZA [auth J]

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, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/M33HTY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.51	α = 90
b = 125.51	β = 90
c = 181.45	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: 2009-07-07

Deposition Author(s):

Joint Center for Structural Genomics

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, 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: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-02-01
Changes: Database references, Derived calculations