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- PDB-4kpk: Crystal structure of a enoyl-CoA hydratase from Shewanella pealea... -

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Basic information

Entry
Database: PDB / ID: 4kpk
TitleCrystal structure of a enoyl-CoA hydratase from Shewanella pealeana ATCC 700345
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsISOMERASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / enoyl-CoA hydratase
Function / homology
Function and homology information


isoprenoid catabolic process / isomerase activity
Similarity search - Function
: / 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 / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesShewanella pealeana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 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 a enoyl-CoA hydratase from Shewanella pealeana ATCC 700345
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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 / 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_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4972
Polymers35,4351
Non-polymers621
Water1,802100
1
A: Enoyl-CoA hydratase/isomerase
hetero molecules

A: Enoyl-CoA hydratase/isomerase
hetero molecules

A: Enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4926
Polymers106,3053
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12840 Å2
ΔGint-80 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.254, 106.254, 61.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/isomerase


Mass: 35435.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella pealeana (bacteria) / Strain: ATCC 700345 / Gene: Spea_2799 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: A8H6D2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M Tris 25% PEG 4000 and 5% Ethylene glycol, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2013 / Details: mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 14646 / Num. obs: 14646 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1119 / % possible all: 72.5

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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: 2.09→36.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.4 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22799 720 4.9 %RANDOM
Rwork0.16775 ---
obs0.17071 13926 95.22 %-
all-13926 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.186 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-1.69 Å20 Å2
2---1.69 Å2-0 Å2
3---5.47 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 4 100 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192099
X-RAY DIFFRACTIONr_bond_other_d0.0010.022034
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9742830
X-RAY DIFFRACTIONr_angle_other_deg0.88934667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56725.098102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 39 -
Rwork0.21 746 -
obs--69.84 %

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