2POD | pdb_00002pod

Crystal structure of a member of enolase superfamily from Burkholderia pseudomallei K96243

PDB DOI: https://doi.org/10.2210/pdb2POD/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Burkholderia pseudomallei K96243
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-26 Released: 2007-06-05
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Ozyurt, S., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.275 (Depositor), 0.270 (DCC)
R-Value Work:
0.209 (Depositor), 0.205 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Member of Enolase Superfamily from Burkholderia Pseudomallei.

Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Gheyi, M., Ozyurt, S., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 92.45 kDa
Atom Count: 6,132
Modeled Residue Count: 759
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase / muconate lactonizing enzyme	A, B	410	Burkholderia pseudomallei K96243	Mutation(s): 8 Gene Names: BPSS2072
UniProt
Find proteins for Q63IJ7 (Burkholderia pseudomallei (strain K96243)) Explore Q63IJ7 Go to UniProtKB: Q63IJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63IJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 2.34 Å
R-Value Free: 0.275 (Depositor), 0.270 (DCC)
R-Value Work: 0.209 (Depositor), 0.205 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.771	α = 90
b = 146.771	β = 90
c = 85.531	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary