4MG4 | pdb_00004mg4

Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315

PDB DOI: https://doi.org/10.2210/pdb4MG4/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-28 Released: 2013-09-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.196 (DCC)
R-Value Work:
0.158 (Depositor), 0.169 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315

Lukacs, C.M., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 222.73 kDa
Atom Count: 16,446
Modeled Residue Count: 1,998
Deposited Residue Count: 2,088
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphonomutase	A, B, C, D, E A, B, C, D, E, F, G, H	261	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BceJ2315_40480, BCAM0587
UniProt
Find proteins for B4EL08 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EL08 Go to UniProtKB: B4EL08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4EL08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain HA [auth H] SDF format, chain R [auth D] SDF format, chain V [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain HA [auth H] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain HA [auth H] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E]	AA [auth F], HA [auth H], R [auth D], V [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain HA [auth H] Focus chain R [auth D] Focus chain V [auth E] Interactions & Density Focus chain AA [auth F] Focus chain HA [auth H] Focus chain R [auth D] Focus chain V [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain S [auth D] SDF format, chain IA [auth H] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain S [auth D] MOL2 format, chain IA [auth H] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain S [auth D] mmCIF format, chain IA [auth H]	BA [auth F] CA [auth F] DA [auth F] EA [auth G] FA [auth G] BA [auth F], CA [auth F], DA [auth F], EA [auth G], FA [auth G], GA [auth G], I [auth A], IA [auth H], J [auth A], JA [auth H], K [auth A], KA [auth H], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth D], W [auth E], X [auth E], Y [auth E], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.189 (Depositor), 0.196 (DCC)
R-Value Work: 0.158 (Depositor), 0.169 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.6	α = 90
b = 91.18	β = 91.53
c = 110.01	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-09-25
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description