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- PDB-4kd6: Crystal structure of a Enoyl-CoA hydratase/isomerase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4kd6
TitleCrystal structure of a Enoyl-CoA hydratase/isomerase from Burkholderia graminis C4D1M
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / PROTEIN STRUCTURE INITIATIVE / alpha/beta / trimeric assembly / lipid metabolism / Crotonase superfamily / enoyl-CoA
Function / homology
Function and homology information


short-chain-enoyl-CoA hydratase / isomerase activity / lyase 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 speciesBurkholderia graminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 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/isomerase from Burkholderia graminis C4D1M
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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/isomerase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water1,38777
1
A: Enoyl-CoA hydratase/isomerase

A: Enoyl-CoA hydratase/isomerase

A: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)94,3613
Polymers94,3613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6420 Å2
ΔGint-40 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.481, 118.481, 38.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/isomerase


Mass: 31453.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia graminis (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_6579 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: B1GB42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% Dioxane, pH 7.0, 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: Apr 19, 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: 2.25→50 Å / Num. all: 15059 / Num. obs: 15059 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 20.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 16 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Num. unique all: 1451 / % possible all: 97.4

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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: 2.25→38.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.384 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22969 759 5.1 %RANDOM
Rwork0.17907 ---
obs0.18161 14225 99.16 %-
all-14225 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.859 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 0 77 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191699
X-RAY DIFFRACTIONr_bond_other_d0.0030.021662
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9782298
X-RAY DIFFRACTIONr_angle_other_deg0.91933805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63322.89576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.111518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
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: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 47 -
Rwork0.276 967 -
obs--91.11 %

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