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- PDB-3ju1: Crystal Structure of Enoyl-CoA Hydratase/Isomerase Family Protein -

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Basic information

Entry
Database: PDB / ID: 3ju1
TitleCrystal Structure of Enoyl-CoA Hydratase/Isomerase Family Protein
ComponentsEnoyl-CoA hydratase/isomerase family protein
Keywordslyase / isomerase / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / L-valine catabolic process
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
ACETIC ACID / FORMIC ACID / 3-hydroxyisobutyryl-CoA hydrolase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Enoyl-CoA Hydratase/Isomerase Family Protein
Authors: Kim, Y. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 9, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,97810
Polymers90,5362
Non-polymers4428
Water7,638424
1
A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5125
Polymers45,2681
Non-polymers2444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4665
Polymers45,2681
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.982, 83.982, 277.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Enoyl-CoA hydratase/isomerase family protein


Mass: 45267.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1681 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q8EGC3
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 2 M sodium formate, 1/10 V8 protease, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→36.06 Å / Num. all: 50834 / Num. obs: 50834 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 33.24 Å2 / Rsym value: 0.081 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 9 % / Mean I/σ(I) obs: 5 / Num. unique all: 2566 / Rsym value: 0.532 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_147)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.301→36.058 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2572 5.09 %random
Rwork0.193 ---
all0.195 50490 --
obs0.195 50490 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.727 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9628 Å2-0 Å2-0 Å2
2--1.9628 Å20 Å2
3----3.9257 Å2
Refinement stepCycle: LAST / Resolution: 2.301→36.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 29 424 5953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175743
X-RAY DIFFRACTIONf_angle_d1.6527804
X-RAY DIFFRACTIONf_dihedral_angle_d16.7792042
X-RAY DIFFRACTIONf_chiral_restr0.095900
X-RAY DIFFRACTIONf_plane_restr0.006997
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3006-2.38280.2762760.20674684496098
2.3828-2.47810.25652780.18464778100
2.4781-2.59090.27442730.20224811100
2.5909-2.72750.28892530.21094835100
2.7275-2.89830.27242310.20434879100
2.8983-3.12190.25932350.20874887100
3.1219-3.43590.23632670.20284842100
3.4359-3.93250.21862180.1847406182
3.9325-4.95250.18612540.1574497399
4.9525-36.06210.18882870.17865168100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.85480.1837-1.26960.53250.08811.217-0.19670.2799-0.1802-0.00410.04250.03970.0805-0.2540.12550.1032-0.02140.05430.1407-0.02940.127426.975439.1046104.5475
21.0795-0.7155-0.40541.03960.14930.9913-0.0301-0.08360.09150.06780.0401-0.11470.03020.2766-0.00940.08580.01070.02620.16250.00340.1014
Refinement TLS groupSelection details: chain B

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