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- PDB-1cw7: LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOC... -

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Basic information

Entry
Database: PDB / ID: 1cw7
TitleLOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOCITRATE
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Isocitrate Dehydrogenase / mutant
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOCITRIC ACID / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsStroud, M.R. / Finer-Moore, J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase.
Authors: Cherbavaz, D.B. / Lee, M.E. / Stroud, R.M. / Koshland Jr., D.E.
#1: Journal: Biochemistry / Year: 1991
Title: Catalytic Mechanism of Nadp+-Dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-Isocitrate and Nadp+ Complexes
Authors: Hurley, J.H. / Dean, A.M. / Koshland Jr., D.E. / Stroud, R.M.
#2: Journal: Biochemistry / Year: 1993
Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex
Authors: Stoddard, B.L. / Dean, A. / Koshland Jr., D.E.
History
DepositionAug 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_sheet.number_strands / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0644
Polymers45,7511
Non-polymers3123
Water4,972276
1
A: ISOCITRATE DEHYDROGENASE
hetero molecules

A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1288
Polymers91,5032
Non-polymers6256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8210 Å2
ΔGint-86 kcal/mol
Surface area30950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.8, 102.8, 150.1
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ISOCITRATE DEHYDROGENASE /


Mass: 45751.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: E. COLI STRAIN JLK1 DEFICIENT IN WILD-TYPE ISOCITRATE DEHYDROGENASE GENE
Plasmid: PTK513 / Production host: Escherichia coli (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ICT / ISOCITRIC ACID / Isocitric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: MG-ISOCITRATE, AMMONIUM SULFATE, DTT, NAN3, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
138-55 %satammonium sulfate1reservoir
21 mMdithiothreitol1reservoir
30.02 %(v/v)1reservoirNaN3
41 mMmeta-ligand solution1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→6.87 Å / Num. all: 19141 / Num. obs: 19141 / % possible obs: 75.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9
Reflection
*PLUS
Num. measured all: 25364

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.6→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 --RANDOM
Rwork0.152 ---
all0.152 19171 --
obs0.152 19171 75.1 %-
Refinement stepCycle: LAST / Resolution: 2.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 19 276 3478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
LS refinement shell
*PLUS
Highest resolution: 2.58 Å / Lowest resolution: 2.8 Å / Rfactor Rwork: 0.188

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