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- PDB-1sv6: Crystal structure of 2-hydroxypentadienoic acid hydratase from Es... -

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Basic information

Entry
Database: PDB / ID: 1sv6
TitleCrystal structure of 2-hydroxypentadienoic acid hydratase from Escherichia Coli
Components2-keto-4-pentenoate hydratase
KeywordsLYASE / Hydratase / Structural genomics / NYSGXRC target T795 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


2-oxopent-4-enoate hydratase / 2-oxopent-4-enoate hydratase activity / 3-phenylpropionate catabolic process / manganese ion binding / identical protein binding / cytoplasm
Similarity search - Function
2-keto-4-pentenoate hydratase / : / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-keto-4-pentenoate hydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sharp, A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of 2-hydroxypentadienoic acid hydratase from Escherichia Coli
Authors: Fedorov, A.A. / Fedorov, E.V. / Sharp, A. / Almo, S.C.
History
DepositionMar 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-keto-4-pentenoate hydratase
B: 2-keto-4-pentenoate hydratase
C: 2-keto-4-pentenoate hydratase
D: 2-keto-4-pentenoate hydratase
E: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)144,5995
Polymers144,5995
Non-polymers00
Water00
1
A: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)28,9201
Polymers28,9201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)28,9201
Polymers28,9201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)28,9201
Polymers28,9201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)28,9201
Polymers28,9201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 2-keto-4-pentenoate hydratase


Theoretical massNumber of molelcules
Total (without water)28,9201
Polymers28,9201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.222, 121.507, 111.796
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein
2-keto-4-pentenoate hydratase / 2-hydroxypentadienoic acid hydratase


Mass: 28919.824 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MHPD, B0350 / Production host: Escherichia coli (E. coli)
References: UniProt: P77608, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, isopropanol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 31828 / Num. obs: 31828 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 1576 RANDOM
Rwork0.239 --
all0.243 31828 -
obs0.243 31828 -
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9890 0 0 0 9890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.32

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