2Q14 | pdb_00002q14

Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb2Q14/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-23 Released: 2007-06-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.254 (DCC)
R-Value Work:
0.207 (Depositor), 0.212 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 385.53 kDa
Atom Count: 27,697
Modeled Residue Count: 3,216
Deposited Residue Count: 3,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphohydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	410	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 13 Gene Names: BT_4208
UniProt
Find proteins for Q8A013 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A013 Go to UniProtKB: Q8A013
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A013
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain X [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain AA [auth H] MOL2 format, chain X [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth H] mmCIF format, chain X [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	AA [auth H] J [auth A] M [auth B] P [auth C] S [auth D] AA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], U [auth E], W [auth F], X [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain T [auth D] SDF format, chain BA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] MOL2 format, chain BA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain T [auth D] mmCIF format, chain BA [auth H]	BA [auth H], N [auth B], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain N [auth B] Focus chain T [auth D] Interactions & Density Focus chain BA [auth H] Focus chain N [auth B] Focus chain T [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Y [auth G] SDF format, chain Z [auth G] SDF format, chain V [auth E] SDF format, chain Q [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain V [auth E] MOL2 format, chain Q [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain V [auth E] mmCIF format, chain Q [auth C]	K [auth A] L [auth A] Q [auth C] V [auth E] Y [auth G] K [auth A], L [auth A], Q [auth C], V [auth E], Y [auth G], Z [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth D] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C]	I [auth A], O [auth C], R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain R [auth D]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.254 (DCC)
R-Value Work: 0.207 (Depositor), 0.212 (DCC)
R-Value Observed: 0.210 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.436	α = 90
b = 137.504	β = 90
c = 279.051	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-06-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-06-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.6: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary