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- PDB-3ucf: Crystal structure of a small-chain dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3ucf
TitleCrystal structure of a small-chain dehydrogenase
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Small-chain dehydrogenase Rossmann Fold
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / identical protein binding
Similarity search - Function
: / 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
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.347 Å
AuthorsBuysschaert, G. / Verstraete, K. / Savvides, S. / Vergauwen, B.
CitationJournal: Febs J. / Year: 2013
Title: Structural and biochemical characterization of an atypical short-chain dehydrogenase/reductase reveals an unusual cofactor preference.
Authors: Buysschaert, G. / Verstraete, K. / Savvides, S.N. / Vergauwen, B.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydrogenase
B: Dehydrogenase
C: Dehydrogenase
D: Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)94,7244
Polymers94,7244
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-102 kcal/mol
Surface area27210 Å2
MethodPISA
2
A: Dehydrogenase
C: Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)47,3622
Polymers47,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-28 kcal/mol
Surface area16650 Å2
MethodPISA
3
A: Dehydrogenase
B: Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)47,3622
Polymers47,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-20 kcal/mol
Surface area16410 Å2
MethodPISA
4
B: Dehydrogenase
D: Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)47,3622
Polymers47,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-28 kcal/mol
Surface area15720 Å2
MethodPISA
5
C: Dehydrogenase
D: Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)47,3622
Polymers47,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-22 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.360, 122.890, 63.140
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dehydrogenase


Mass: 23680.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VVA-1599, VVA1599 / Plasmid: pACYCDUet-I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MBY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 10% PEG 3350, 0.2 M BIS-TRIS pH 6.5, Protein concentration: 8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.347→45 Å / Num. all: 35379 / Num. obs: 34318 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 29.17 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 10.57
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.74 / Num. unique all: 5671 / % possible all: 94.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O5I

1o5i


Resolution: 2.347→42.524 Å / SU ML: 0.5 / Isotropic thermal model: isotropic - 1 B-factor per atom / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1712 4.99 %Random
Rwork0.1808 ---
obs0.1823 34312 97.26 %-
all-35379 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.741 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 36.63 Å2
Baniso -1Baniso -2Baniso -3
1--3.7327 Å20 Å2-5.9908 Å2
2--4.0418 Å20 Å2
3----0.3091 Å2
Refinement stepCycle: LAST / Resolution: 2.347→42.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5615 0 0 273 5888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025704
X-RAY DIFFRACTIONf_angle_d0.6677759
X-RAY DIFFRACTIONf_dihedral_angle_d13.3161922
X-RAY DIFFRACTIONf_chiral_restr0.038953
X-RAY DIFFRACTIONf_plane_restr0.002968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3471-2.41610.28791330.24952594X-RAY DIFFRACTION94
2.4161-2.49410.29361400.22712656X-RAY DIFFRACTION96
2.4941-2.58320.25731430.21522715X-RAY DIFFRACTION97
2.5832-2.68660.24291420.19612689X-RAY DIFFRACTION97
2.6866-2.80890.23851440.20082734X-RAY DIFFRACTION98
2.8089-2.9570.2191430.1912723X-RAY DIFFRACTION98
2.957-3.14220.22941440.18512733X-RAY DIFFRACTION98
3.1422-3.38470.20951430.18832714X-RAY DIFFRACTION98
3.3847-3.72510.20931450.16912756X-RAY DIFFRACTION98
3.7251-4.26370.16981440.15142751X-RAY DIFFRACTION98
4.2637-5.37010.16591450.14922754X-RAY DIFFRACTION98
5.3701-42.53080.19681460.18272781X-RAY DIFFRACTION98

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