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- PDB-3ksu: Crystal structure of short-chain dehydrogenase from oenococcus oe... -

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Basic information

Entry
Database: PDB / ID: 3ksu
TitleCrystal structure of short-chain dehydrogenase from oenococcus oeni psu-1
Components3-oxoacyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / DEHYDROGENASE / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homologyoxidoreductase activity, acting on CH-OH group of donors / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 3-oxoacyl-acyl carrier protein reductase
Function and homology information
Biological speciesOenococcus oeni PSU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Short-Chain Dehydrogenase from Oenococcus Oeni Psu-1
Authors: Patskovsky, Y. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-acyl carrier protein reductase
B: 3-oxoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)58,1822
Polymers58,1822
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-15 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.589, 84.207, 87.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein 3-oxoacyl-acyl carrier protein reductase


Mass: 29090.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oenococcus oeni PSU-1 (bacteria) / Strain: BAA-331 / PSU-1 / Gene: OEOE_0078 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04HJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS PH 5.5, 25% PEG3350, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→40 Å / Num. obs: 23892 / % possible obs: 94.9 % / Observed criterion σ(I): -5 / Redundancy: 3.5 % / Biso Wilson estimate: 52.407 Å2 / Rsym value: 0.1 / Net I/σ(I): 5.2
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
SHELXmodel building
PHENIXmodel building
RESOLVEmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
PHENIXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.363 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 734 3.3 %RANDOM
Rwork0.23 ---
obs0.232 21755 94.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2--2.08 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 0 86 3651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9464911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26926.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1615641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.827153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1360.31528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.52440
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.5222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.330
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7322344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2933643
X-RAY DIFFRACTIONr_scbond_it5.92541468
X-RAY DIFFRACTIONr_scangle_it8.35461267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1661 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.330.3
tight thermal5.235
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 46 -
Rwork0.28 1460 -
obs--87.15 %

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