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- PDB-3ctv: Crystal structure of central domain of 3-hydroxyacyl-CoA dehydrog... -

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Basic information

Entry
Database: PDB / ID: 3ctv
TitleCrystal structure of central domain of 3-hydroxyacyl-CoA dehydrogenase from Archaeoglobus fulgidus
Components3-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / APC7539 / 3-hydroxyacyl-CoA dehydrogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Fatty acid metabolism / Lipid metabolism / Lyase / Multifunctional enzyme / NAD
Function / homology
Function and homology information


enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / membrane => GO:0016020
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of central domain of 3-hydroxyacyl-CoA dehydrogenase from Archaeoglobus fulgidus.
Authors: Osipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2652
Polymers12,1691
Non-polymers961
Water543
1
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5304
Polymers24,3372
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_656-x+3/2,y,-z+11
Buried area2030 Å2
ΔGint-19.6 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.464, 101.464, 101.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase / Hbd-10


Mass: 12168.692 Da / Num. of mol.: 1 / Fragment: Central domain: Residues 295-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304 / VC-16 / JCM 9628 / NBRC 100126 / Gene: AF_2273 / Plasmid: Modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28011
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5 M Ammonium sulfate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 30, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→32.1 Å / Num. all: 6516 / Num. obs: 6516 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.325 / Net I/σ(I): 12.4
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.49 / Num. unique all: 541 / Χ2: 0.936 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.46→32.1 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING WITH A TWIN FRACTION OF 0.317 AND WITH A TWIN LAW OF K,H,-L.
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 299 -Random
Rwork0.1935 ---
all-6097 --
obs-6097 98.11 %-
Displacement parametersBiso mean: 73.624 Å2
Refinement stepCycle: LAST / Resolution: 2.46→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms721 0 5 3 729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.308

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