4DLL | pdb_00004dll

Crystal structure of a 2-hydroxy-3-oxopropionate reductase from Polaromonas sp. JS666

PDB DOI: https://doi.org/10.2210/pdb4DLL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Polaromonas sp. JS666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-06 Released: 2012-02-15
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.278 (Depositor), 0.280 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a 2-hydroxy-3-oxopropionate reductase from Polaromonas sp. JS666

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 69.15 kDa
Atom Count: 4,240
Modeled Residue Count: 573
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxy-3-oxopropionate reductase	A, B	320	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro_1712 EC: 1.1.1.60
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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: 2.11 Å
R-Value Free: 0.278 (Depositor), 0.280 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.868	α = 92.14
b = 47.01	β = 95.3
c = 77.498	γ = 101.19

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHASER	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary