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- PDB-1wz8: Crystal Structure of Probable Enoyl-CoA Dehydratase from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 1wz8
TitleCrystal Structure of Probable Enoyl-CoA Dehydratase from Thermus Thermophilus HB8
Componentsenoyl-CoA hydratase
KeywordsLYASE / Crotonase / CoA / Hexamer / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Probable Enoyl-CoA Dehydratase from Thermus Thermophilus HB8
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionMar 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: enoyl-CoA hydratase
C: enoyl-CoA hydratase
D: enoyl-CoA hydratase
E: enoyl-CoA hydratase
F: enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,95914
Polymers173,0136
Non-polymers9458
Water27,8871548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27660 Å2
ΔGint-282 kcal/mol
Surface area47200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.485, 127.065, 146.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer

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Components

#1: Protein
enoyl-CoA hydratase / Probable enoyl-CoA dehydratase


Mass: 28835.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLS5, enoyl-CoA hydratase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1548 / 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: 2.04 Å3/Da / Density % sol: 0.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.85
Details: MPD, MES, NaOH, pH 5.85, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 16, 2004 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 131899 / Num. obs: 131809 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 4.3 / Num. unique all: 12123 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IUY

1iuy


Resolution: 1.8→39.14 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 6585 -RANDOM
Rwork0.2235 ---
all-131899 --
obs-131809 99.5 %-
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20 Å2
2--1.6 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12180 0 64 1548 13792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_improper_angle_d0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.8-1.870.3155990.2680.0131291898.3
1.87-1.940.2756250.250.0111306199.7
1.94-2.030.2856590.2410.0111309999.7
2.03-2.140.2666660.2380.011311299.7
2.14-2.270.2556330.220.011313599.8
2.27-2.440.2596530.220.011316699.8

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