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- PDB-3kux: Structure of the YPO2259 putative oxidoreductase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3kux
TitleStructure of the YPO2259 putative oxidoreductase from Yersinia pestis
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / oxidoreductase family / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxidoreductase / Putative oxidoreductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Gordon, E. / Kwon, K. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of the YPO2259 putative oxidoreductase from Yersinia pestis
Authors: Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Kwon, K. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7552
Polymers38,7201
Non-polymers351
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5114
Polymers77,4402
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2930 Å2
ΔGint-16 kcal/mol
Surface area29300 Å2
MethodPISA
3
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5114
Polymers77,4402
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area1780 Å2
ΔGint-15 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.55, 97.55, 172.51
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative oxidoreductase / / Putative uncharacterized protein


Mass: 38719.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: mviM4, y2101, YPO2259, YP_2055 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q7CIK0, UniProt: A0A3N4BF22*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% Tacsimate, 10mM magnesium chloride, 100mM HEPES, 300mM NDSB-195, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2009 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 13362 / Num. obs: 13282 / % possible obs: 99.4 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.098 / Χ2: 0.988 / Net I/σ(I): 8.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1267 / Χ2: 1 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→46.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 25.893 / SU ML: 0.233 / SU R Cruickshank DPI: 0.735 / SU Rfree: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.2 / ESU R: 0.73 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 655 4.9 %RANDOM
Rwork0.199 ---
all0.2 13314 --
obs0.2 13251 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.2 Å2 / Biso mean: 22.948 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 1 44 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222776
X-RAY DIFFRACTIONr_angle_refined_deg0.7961.9643787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9415349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96524.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.631514
X-RAY DIFFRACTIONr_chiral_restr0.0550.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212127
X-RAY DIFFRACTIONr_mcbond_it1.3441.51742
X-RAY DIFFRACTIONr_mcangle_it2.50322806
X-RAY DIFFRACTIONr_scbond_it3.9131034
X-RAY DIFFRACTIONr_scangle_it6.0264.5980
LS refinement shellResolution: 2.75→2.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 42 -
Rwork0.309 903 -
all-945 -
obs-838 99.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5705-2.0549-1.51386.7646-1.55272.19420.4125-0.3539-1.2161-0.65610.43361.36490.15780.0197-0.8460.2717-0.0182-0.28260.13510.00230.3822-7.92932.017-12.823
27.3177-2.8838-0.25977.1543-0.55311.29440.95250.1256-1.7359-0.7758-0.03161.24430.58360.2595-0.9210.37940.0986-0.47980.1477-0.04440.5562-2.7424.678-13.113
30.8232-0.33610.76751.82080.87841.27640.19270.2642-0.1199-0.2466-0.0782-0.0389-0.09370.2516-0.11450.31820.0479-0.01460.3651-0.02930.08377.77944.102-6.556
42.8249-0.70630.6192-5.6549-5.17996.19320.04110.8805-1.2205-1.3121-0.00610.90861.3806-0.4029-0.0350.6387-0.1160.0140.4072-0.15960.7031-1.37631.40312.601
50.9014-0.02020.72090.4090.4821.12420.0390.0179-0.0616-0.10690.0427-0.0221-0.08-0.0986-0.08170.28030.0103-0.00350.30540.02280.10162.20148.4123.161
65.9625-0.18057.74090.78570.11619.84720.160.7997-0.148-0.080.0225-0.16860.01830.9028-0.18260.24680.04330.04770.3765-0.08360.069114.86838.43-4.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2A27 - 99
3X-RAY DIFFRACTION3A100 - 151
4X-RAY DIFFRACTION4A152 - 171
5X-RAY DIFFRACTION5A172 - 307
6X-RAY DIFFRACTION6A308 - 349

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