2FKN

crystal structure of urocanase from bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb2FKN/pdb

Classification: LYASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-01-05 Released: 2007-01-02
Deposition Author(s): Yu, Y.-M., Liang, Y.-H., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.256 (Depositor), 0.250 (DCC)
R-Value Work:
0.205 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Urocanase from Bacillus Subtilis

Yu, Y.-M., Liang, Y.-H., Su, X.-D.

To be published.

Macromolecule Content

Total Structure Weight: 245.6 kDa
Atom Count: 17,568
Modelled Residue Count: 2,178
Deposited Residue Count: 2,208
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urocanate hydratase	A, B, C, D	552	Bacillus subtilis	Mutation(s): 0 Gene Names: hutU EC: 4.2.1.49
UniProt
Find proteins for P25503 (Bacillus subtilis (strain 168)) Explore P25503 Go to UniProtKB: P25503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25503
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.256 (Depositor), 0.250 (DCC)
R-Value Work: 0.205 (Depositor), 0.200 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.791	α = 90
b = 131.268	β = 90
c = 164.696	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
HLK	data reduction
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-01-02

Deposition Author(s):

Yu, Y.-M.

Liang, Y.-H.

Su, X.-D.

Revision History (Full details and data files)

Version 1.0: 2007-01-02
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2014-11-12
Changes: Structure summary
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2024-03-13
Changes: Data collection, Database references, Derived calculations