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- PDB-1j1w: Crystal Structure Of The Monomeric Isocitrate Dehydrogenase In Co... -

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Basic information

Entry
Database: PDB / ID: 1j1w
TitleCrystal Structure Of The Monomeric Isocitrate Dehydrogenase In Complex With NADP+
ComponentsIsocitrate Dehydrogenase
KeywordsOXIDOREDUCTASE / Greek key motif
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Monomeric Isocitrate Dehydrogenase in the Presence of NADP+
Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
#1: Journal: Structure / Year: 2002
Title: Structure of the Monomeric Isocitrate Dehydrogenase: Evidence of a Protein Monomerization by a Domain Duplication
Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase by the MAD method using Mn atoms
Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
History
DepositionDec 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Isocitrate Dehydrogenase
B: Isocitrate Dehydrogenase
C: Isocitrate Dehydrogenase
D: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,0048
Polymers322,0314
Non-polymers2,9744
Water8,017445
1
A: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2512
Polymers80,5081
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2512
Polymers80,5081
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2512
Polymers80,5081
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isocitrate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2512
Polymers80,5081
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.496, 110.407, 133.698
Angle α, β, γ (deg.)90.000, 90.156, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isocitrate Dehydrogenase


Mass: 80507.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: IAM1078
References: UniProt: P16100, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, HEPES-NaOH, CaCl2, NADP+, Isocitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
2100 mMHEPES-NaOH1droppH7.0
310 %(v/v)glycerol1drop
4100 mMHEPES-NaOH1reservoirpH7.0
524-28 %(w/v)PEG60001reservoir
620 %(v/v)glycerol1reservoir
71-10 mM2R, 3S-isocitrate1reservoir
81-10 mM1reservoirCaCl2
91-10 mMbeta-NADP+1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2002
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 57614 / Num. obs: 52458 / % possible obs: 96.2 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 55.7 Å2 / Rsym value: 0.092 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7347 / Rsym value: 0.323 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 178630 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 92.8 % / Rmerge(I) obs: 0.385

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ITW

1itw


Resolution: 3.2→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 4645 9.9 %RANDOM
Rwork0.26 ---
all-50708 --
obs-46930 88.8 %-
Solvent computationSolvent model: throughout / Bsol: 36.4 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.61 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å20 Å20.949 Å2
2---17.439 Å20 Å2
3---21.029 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22544 0 192 445 23181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008059
X-RAY DIFFRACTIONc_angle_deg1.52682
X-RAY DIFFRACTIONc_dihedral_angle_d22.13408
X-RAY DIFFRACTIONc_improper_angle_d0.98993
X-RAY DIFFRACTIONc_mcbond_it1.04
X-RAY DIFFRACTIONc_mcangle_it1.25
X-RAY DIFFRACTIONc_scbond_it1.84
X-RAY DIFFRACTIONc_scangle_it2.03
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 351 9.4 %
Rwork0.333 3372 -
obs-3723 70.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0081
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.13
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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