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- PDB-3hin: CRYSTAL STRUCTURE OF putative enoyl-CoA hydratase from Rhodopseud... -

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Basic information

Entry
Database: PDB / ID: 3hin
TitleCRYSTAL STRUCTURE OF putative enoyl-CoA hydratase from Rhodopseudomonas palustris CGA009
ComponentsPutative 3-hydroxybutyryl-CoA dehydratase
KeywordsLYASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / enoyl-CoA hydratase / Rhodopseudomonas palustris / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydratase / fatty acid beta-oxidation / lyase activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / 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 / Orthogonal Bundle ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxybutyryl-CoA dehydratase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative enoyl-CoA hydratase from Rhodopseudomonas palustris CGA009
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Putative 3-hydroxybutyryl-CoA dehydratase
B: Putative 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)58,8912
Polymers58,8912
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative 3-hydroxybutyryl-CoA dehydratase
B: Putative 3-hydroxybutyryl-CoA dehydratase

A: Putative 3-hydroxybutyryl-CoA dehydratase
B: Putative 3-hydroxybutyryl-CoA dehydratase

A: Putative 3-hydroxybutyryl-CoA dehydratase
B: Putative 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)176,6746
Polymers176,6746
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area26880 Å2
ΔGint-202 kcal/mol
Surface area53330 Å2
MethodPISA
3
A: Putative 3-hydroxybutyryl-CoA dehydratase

A: Putative 3-hydroxybutyryl-CoA dehydratase

A: Putative 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)88,3373
Polymers88,3373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10170 Å2
ΔGint-69 kcal/mol
Surface area30770 Å2
MethodPISA
4
B: Putative 3-hydroxybutyryl-CoA dehydratase

B: Putative 3-hydroxybutyryl-CoA dehydratase

B: Putative 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)88,3373
Polymers88,3373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10650 Å2
ΔGint-66 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.111, 124.111, 124.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Putative 3-hydroxybutyryl-CoA dehydratase


Mass: 29445.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1786 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q6N8W7, 3-hydroxybutyryl-CoA dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1 M TRIS HCL, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 32.16 / Number: 197214 / Rmerge(I) obs: 0.127 / Χ2: 7.31 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 42495 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785098.210.0576.8455.1
5.386.7810010.0968.9835.2
4.75.3899.810.11112.3064.8
4.274.799.910.11714.924.8
3.974.2799.910.12614.2794.7
3.733.9799.310.13614.24.5
3.553.739910.15414.8664
3.393.5599.910.16610.5434.6
3.263.3910010.1798.5974.7
3.153.2699.910.196.9914.7
3.053.1510010.225.9674.7
2.963.0510010.2314.9974.7
2.892.9610010.2574.2964.7
2.822.8910010.273.9724.6
2.752.8210010.313.2244.6
2.692.7599.910.3322.8524.6
2.642.6910010.3872.2834.5
2.592.6410010.4232.1954.5
2.542.5910010.4961.9894.5
2.52.5410010.5161.8884.4
ReflectionResolution: 2→50 Å / Num. obs: 42979 / % possible obs: 99.8 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.127 / Χ2: 7.308 / Net I/σ(I): 32.157
Reflection shellResolution: 2→2.03 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.516 / Num. unique all: 2149 / Χ2: 1.888 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.718 / SU B: 13.366 / SU ML: 0.158 / SU R Cruickshank DPI: 0.206 / SU Rfree: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1929 5.1 %RANDOM
Rwork0.225 ---
obs0.227 38103 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.78 Å2 / Biso mean: 41.015 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 0 242 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223863
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9695239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7723.418158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87315640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3791532
X-RAY DIFFRACTIONr_chiral_restr0.1470.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212896
X-RAY DIFFRACTIONr_mcbond_it1.1731.52515
X-RAY DIFFRACTIONr_mcangle_it2.01124011
X-RAY DIFFRACTIONr_scbond_it3.18331348
X-RAY DIFFRACTIONr_scangle_it4.784.51228
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 166 -
Rwork0.294 2929 -
all-3095 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.76690.2606-0.12321.2205-0.08270.7509-0.06290.061-0.1636-0.04520.0213-0.00720.21070.02920.04160.10590.02390.01880.0159-0.00950.039564.596841.299963.945
20.56530.0717-0.04220.74670.28650.98670.0031-0.04190.14440.1412-0.01990.1137-0.116-0.04350.01680.06320.00230.0290.0086-0.02140.076160.657982.578184.4665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 266
2X-RAY DIFFRACTION1A276 - 406
3X-RAY DIFFRACTION2B11 - 261
4X-RAY DIFFRACTION2B276 - 386

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