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- PDB-4dqx: Crystal structure of a short chain dehydrogenase from Rhizobium e... -

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Basic information

Entry
Database: PDB / ID: 4dqx
TitleCrystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42
ComponentsProbable oxidoreductase protein
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Probable oxidoreductase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHenix_autosol / Resolution: 2 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Siedel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable oxidoreductase protein
B: Probable oxidoreductase protein
C: Probable oxidoreductase protein
D: Probable oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)119,8774
Polymers119,8774
Non-polymers00
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-103 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.245, 64.595, 113.353
Angle α, β, γ (deg.)90.00, 96.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable oxidoreductase protein / Short chain dehydrogenase


Mass: 29969.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: RHE_PD00113 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8KL31
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M MgCl2, 0.1M Hepes, 22% Poly(acrylic sodium salt)5100, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 77843 / Num. obs: 77843 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5
Reflection shellResolution: 2→2.07 Å / Redundancy: 97.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / Num. unique all: 7636 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CBASSdata collection
AutoSolphasing
Cootmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: PHenix_autosol
Starting model: None

Resolution: 2→44.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.949 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A small continuous residual density between Arg 185 of chains C and D and Chains A and B were modeled as waters.
RfactorNum. reflection% reflectionSelection details
Rfree0.19777 3918 5 %RANDOM
Rwork0.1592 ---
obs0.16117 73782 98.5 %-
all-77842 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.098 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 0 653 8052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227497
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.94110137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56851000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28423.3297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.219151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3141564
X-RAY DIFFRACTIONr_chiral_restr0.1760.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025572
X-RAY DIFFRACTIONr_mcbond_it1.2561.54950
X-RAY DIFFRACTIONr_mcangle_it2.08327910
X-RAY DIFFRACTIONr_scbond_it4.35232547
X-RAY DIFFRACTIONr_scangle_it6.4054.52227
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 280 -
Rwork0.194 5254 -
obs--96.46 %

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