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- PDB-3us8: Crystal Structure of an isocitrate dehydrogenase from Sinorhizobi... -

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Basic information

Entry
Database: PDB / ID: 3us8
TitleCrystal Structure of an isocitrate dehydrogenase from Sinorhizobium meliloti 1021
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / PSI-BIOLOGY / Structural Genomics / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / isocitrate dehydrogenase / Rossmann fold / Isocitrate
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, 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 an isocitrate dehydrogenase from Sinorhizobium meliloti 1021
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0714
Polymers96,8782
Non-polymers1922
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-85 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.458, 96.208, 146.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isocitrate dehydrogenase [NADP]


Mass: 48439.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: icd, R01792, SMc00480 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (de3)
References: UniProt: Q92PG6, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M LiSO4, 0.1M hepses pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2011 / Details: mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 46902 / Num. obs: 46902 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.2
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 19 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3849 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.084 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.253 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2366 5.1 %RANDOM
Rwork0.18 ---
all0.207 44470 --
obs0.182 44470 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6332 0 10 363 6705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026480
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.9598764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8824.295298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.327151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3141536
X-RAY DIFFRACTIONr_chiral_restr0.1550.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214890
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 156 -
Rwork0.182 2949 -
obs--97.8 %

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