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- PDB-3k6j: Crystal structure of the dehydrogenase part of multifuctional enz... -

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Basic information

Entry
Database: PDB / ID: 3k6j
TitleCrystal structure of the dehydrogenase part of multifuctional enzyme 1 from C.elegans
ComponentsProtein F01G10.3, confirmed by transcript evidence
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / peroxisome / metal ion binding
Similarity search - Function
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Enoyl-CoA Hydratase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOuyang, Z. / Zhang, K. / Zhai, Y. / Lu, J. / Sun, F.
CitationJournal: To be Published
Title: Crystal structure of the dehydrogenase part of multifuctional enzyme 1 from C.elegans
Authors: Ouyang, Z. / Zhang, K. / Zhai, Y. / Lu, J. / Sun, F.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_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_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: Protein F01G10.3, confirmed by transcript evidence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6926
Polymers52,2461
Non-polymers4455
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.025, 90.657, 66.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein F01G10.3, confirmed by transcript evidence


Mass: 52246.371 Da / Num. of mol.: 1 / Fragment: the dehydrogenase part (UNP residues 7-426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ech-9, F01G10.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O17762
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 0.1M K2HPO4, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 10, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→31.09 Å / Num. all: 24541 / Num. obs: 24533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 26.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2404 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
OASISmodel building
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZCJ

1zcj


Resolution: 2.2→31.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.922 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26734 1230 5 %RANDOM
Rwork0.20971 ---
all0.21256 24489 --
obs0.21256 23225 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---1.44 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 21 176 3626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223529
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9584755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54324.762168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54715653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8181518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212629
X-RAY DIFFRACTIONr_mcbond_it0.7011.52141
X-RAY DIFFRACTIONr_mcangle_it1.323455
X-RAY DIFFRACTIONr_scbond_it1.9331388
X-RAY DIFFRACTIONr_scangle_it3.1434.51298
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 100 -
Rwork0.259 1672 -
obs-1230 99.83 %

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