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- PDB-4j2u: Crystal structure of an enoyl-CoA hydratase from Rhodobacter spha... -

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Basic information

Entry
Database: PDB / ID: 4j2u
TitleCrystal structure of an enoyl-CoA hydratase from Rhodobacter sphaeroides 2.4.1
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / New York Structural Genomics Research Consortium / alpha/beta fold / Hydratase / (3S)-3-hydroxyacyl-CoA
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / L-valine catabolic process / enoyl-CoA hydratase activity / cytosol
Similarity search - Function
Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-hydroxyisobutyryl-CoA hydrolase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of an enoyl-CoA hydratase from Rhodobacter sphaeroides 2.4.1
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)79,4842
Polymers79,4842
Non-polymers00
Water3,549197
1
A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)39,7421
Polymers39,7421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)39,7421
Polymers39,7421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.336, 54.318, 103.460
Angle α, β, γ (deg.)90.00, 123.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 39741.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: ATCC BAA-808, RHOS4_17590, RSP_0155 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J1K7, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 23% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium sulfate,2% Ethylene glycol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 46416 / Num. obs: 46416 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Num. unique all: 2769 / % possible all: 68.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→48.05 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.22 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.189 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24423 2329 5 %RANDOM
Rwork0.18843 ---
obs0.19117 44084 95.3 %-
all-44084 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.438 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-0.31 Å2
2--2.14 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 0 197 5333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195246
X-RAY DIFFRACTIONr_bond_other_d0.0030.025091
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9847126
X-RAY DIFFRACTIONr_angle_other_deg0.931311657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16922.241232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03115778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.021562
X-RAY DIFFRACTIONr_chiral_restr0.1140.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 137 -
Rwork0.232 2282 -
obs--67.91 %

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