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- PDB-1itw: Crystal structure of the monomeric isocitrate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 1itw
TitleCrystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Greece 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
ISOCITRIC ACID / : / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular Replacement method / Resolution: 1.95 Å
AuthorsYasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
Citation
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.
#1: 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
DepositionFeb 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
C: Isocitrate dehydrogenase
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,07413
Polymers322,0314
Non-polymers1,0439
Water41,5432306
1
A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7553
Polymers80,5081
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8104
Polymers80,5081
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7553
Polymers80,5081
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7553
Polymers80,5081
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.4051, 119.0229, 128.2170
Angle α, β, γ (deg.)90.0000, 99.0058, 90.0000
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2306 / 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: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, PEG6000, glycerol, manganese chloride, DL-isocitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 291 K
Details: Yasutake, Y., (2001) Acta Crystallogr., Sect.D, 57, 1682.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MHEPES-NaOH1reservoirpH7.0
224.0 %(w/v)PEG60001reservoir
320.0 %(v/v)glycerol1reservoir
44.0 mM1reservoirMnCl2
54.0 mMDL-isocitrate1reservoir
68.0 mg/mlprotein1drop
70.1 MHEPES-NaOH1droppH7.0
810.0 %(v/v)glycerol1drop

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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: Sep 20, 2001
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 237767 / Num. obs: 235314 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 24.474 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.071 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / Num. unique all: 33505 / Rsym value: 0.327 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 846014
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SHELXSphasing
AMoREphasing
DMmodel building
DMMultimodel building
CNSrefinement
CCP4(SCALA)data scaling
DMphasing
DMMultiphasing
RefinementMethod to determine structure: MAD, Molecular Replacement method
Resolution: 1.95→10 Å / Isotropic thermal model: Isotropic for overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 23269 9.9 %RANDOM
Rwork0.193 ---
all-233612 --
obs-235314 98.9 %-
Solvent computationSolvent model: throughout / Bsol: 69 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 23.5096 Å2
Baniso -1Baniso -2Baniso -3
1--3.913 Å20 Å2-1.92 Å2
2--3.002 Å20 Å2
3---0.911 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22586 0 57 2306 24949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00494
X-RAY DIFFRACTIONc_angle_deg1.22762
X-RAY DIFFRACTIONc_dihedral_angle_d21.65165
X-RAY DIFFRACTIONc_improper_angle_d0.82829
X-RAY DIFFRACTIONc_mcbond_it1.16
X-RAY DIFFRACTIONc_mcangle_it1.68
X-RAY DIFFRACTIONc_scbond_it1.96
X-RAY DIFFRACTIONc_scangle_it2.79
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.264 2325 9.86 %
Rwork0.2254 20444 -
obs-22769 96.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 233612 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.65165
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82829

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