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- PDB-3uce: Crystal structure of a small-chain dehydrogenase in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 3uce
TitleCrystal structure of a small-chain dehydrogenase in complex with NADPH
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Small-chain dehydrogenase
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
Chem-NDP / Dehydrogenase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 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 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Sep 13, 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: Dehydrogenase
B: Dehydrogenase
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7068
Polymers94,7244
Non-polymers2,9824
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-116 kcal/mol
Surface area30480 Å2
MethodPISA
2
A: Dehydrogenase
C: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8534
Polymers47,3622
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-34 kcal/mol
Surface area18070 Å2
MethodPISA
3
A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8534
Polymers47,3622
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-29 kcal/mol
Surface area18470 Å2
MethodPISA
4
B: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8534
Polymers47,3622
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-34 kcal/mol
Surface area18110 Å2
MethodPISA
5
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8534
Polymers47,3622
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-29 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.630, 96.260, 72.110
Angle α, β, γ (deg.)90.00, 103.99, 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: VVA1599 / Plasmid: pACYCDuet-I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MBY8
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 18% PEG-5000, 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: SLS / Beamline: X06SA / Wavelength: 0.99993 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.798→40 Å / Num. all: 85740 / Num. obs: 84971 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.78 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.54
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.41 / Num. unique all: 13760 / % possible all: 97

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Processing

Software
NameVersionClassification
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: 1.798→39.201 Å / SU ML: 0.46 / Isotropic thermal model: isotropic - one B-factor per atom / σ(F): 1.99 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4243 5 %RANDOM
Rwork0.1752 ---
obs0.1773 84914 99.15 %-
all-85740 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.281 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso mean: 24.05 Å2
Baniso -1Baniso -2Baniso -3
1--7.806 Å20 Å2-1.875 Å2
2--0.9844 Å2-0 Å2
3---6.8216 Å2
Refinement stepCycle: LAST / Resolution: 1.798→39.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 192 989 7612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076746
X-RAY DIFFRACTIONf_angle_d1.0969204
X-RAY DIFFRACTIONf_dihedral_angle_d14.4432334
X-RAY DIFFRACTIONf_chiral_restr0.0591104
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7981-1.81850.30421250.27252332X-RAY DIFFRACTION87
1.8185-1.83990.29771470.25462707X-RAY DIFFRACTION100
1.8399-1.86240.31111420.2582686X-RAY DIFFRACTION100
1.8624-1.88590.31581410.24552740X-RAY DIFFRACTION100
1.8859-1.91070.30741310.2342670X-RAY DIFFRACTION100
1.9107-1.93690.2321400.21752695X-RAY DIFFRACTION100
1.9369-1.96460.23891470.21152670X-RAY DIFFRACTION100
1.9646-1.99390.281470.19432745X-RAY DIFFRACTION100
1.9939-2.02510.231420.19612641X-RAY DIFFRACTION100
2.0251-2.05830.27621380.19172728X-RAY DIFFRACTION100
2.0583-2.09380.24061370.19852705X-RAY DIFFRACTION100
2.0938-2.13180.27921460.18852682X-RAY DIFFRACTION100
2.1318-2.17280.20731390.17922719X-RAY DIFFRACTION100
2.1728-2.21720.24641410.17432660X-RAY DIFFRACTION100
2.2172-2.26540.21091430.17162713X-RAY DIFFRACTION100
2.2654-2.31810.23041470.16282726X-RAY DIFFRACTION100
2.3181-2.3760.26651420.16852677X-RAY DIFFRACTION99
2.376-2.44030.21511380.16842669X-RAY DIFFRACTION100
2.4403-2.51210.2191450.16322697X-RAY DIFFRACTION100
2.5121-2.59310.23111400.16582713X-RAY DIFFRACTION100
2.5931-2.68580.20261450.15972725X-RAY DIFFRACTION100
2.6858-2.79330.20721440.15862698X-RAY DIFFRACTION100
2.7933-2.92040.23081420.16192702X-RAY DIFFRACTION99
2.9204-3.07430.21561410.16482702X-RAY DIFFRACTION100
3.0743-3.26680.20371430.17312721X-RAY DIFFRACTION99
3.2668-3.51890.21511400.16812681X-RAY DIFFRACTION99
3.5189-3.87270.19661410.16272664X-RAY DIFFRACTION98
3.8727-4.43250.16131400.14582713X-RAY DIFFRACTION99
4.4325-5.58190.16881450.14952724X-RAY DIFFRACTION99
5.5819-39.20980.1991440.192766X-RAY DIFFRACTION99

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