3FZ5

Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from Rhodobacter sphaeroides

PDB DOI: https://doi.org/10.2210/pdb3FZ5/pdb

Classification: ISOMERASE
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-23 Released: 2009-02-03
Deposition Author(s): Chang, C., Hatzos, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.260
R-Value Work: 0.204
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from Rhodobacter sphaeroides

Chang, C., Hatzos, C., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 92.52 kDa
Atom Count: 6,612
Modelled Residue Count: 754
Deposited Residue Count: 808
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible 2-hydroxychromene-2-carboxylate isomerase	A, B, C, D	202	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: RHOS4_04980, RSP_1916
UniProt
Find proteins for Q3J568 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J568 Go to UniProtKB: Q3J568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3J568
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C]	E [auth A], G [auth B], H [auth C]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.260
R-Value Work: 0.204
R-Value Observed: 0.207
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.769	α = 94.61
b = 48.724	β = 100.46
c = 95.206	γ = 90.1

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing