2OPI | pdb_00002opi

Crystal Structure of L-fuculose-1-phosphate aldolase from Bacteroides thetaiotaomicron

PDB DOI: https://doi.org/10.2210/pdb2OPI/pdb

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

Deposited: 2007-01-29 Released: 2007-02-27
Deposition Author(s): Chang, C., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.225 (Depositor), 0.221 (DCC)
R-Value Observed:
0.227 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of L-fuculose-1-phosphate aldolase from Bacteroides thetaiotaomicron

Chang, C., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 47.56 kDa
Atom Count: 3,228
Modeled Residue Count: 412
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-fuculose-1-phosphate aldolase	A, B	212	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 6 Gene Names: fucA, BT_1274 EC: 4.1.2.17
UniProt
Find proteins for Q9RQ12 (Bacteroides thetaiotaomicron) Explore Q9RQ12 Go to UniProtKB: Q9RQ12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RQ12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 2.50 Å
R-Value Free: 0.260 (Depositor), 0.258 (DCC)
R-Value Work: 0.225 (Depositor), 0.221 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.934	α = 90
b = 115.934	β = 90
c = 73.722	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-02-27
Type: Initial release
Version 1.1: 2007-11-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.