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- PDB-1sjs: ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR B... -

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Basic information

Entry
Database: PDB / ID: 1sjs
TitleACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY DOMAIN SHIFTING
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / I OXIDOREDUCTASE / NAD(A) - CHOH(D) / PHOSPHORYLATION
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / tricarboxylic acid cycle / electron transport chain / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.42 Å
AuthorsFiner-Moore, J. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1997
Title: Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.
Authors: Finer-Moore, J. / Tsutakawa, S.E. / Cherbavaz, D.R. / LaPorte, D.C. / Koshland Jr., D.E. / Stroud, R.M.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-Range Conformational Change in the Free Enzyme
Authors: Hurley, J.H. / Dean, A.M. / Thorsness, P.E. / Koshland Junior, D.E. / Stroud, R.M.
#2: Journal: Science / Year: 1990
Title: Regulation of an Enzyme by Phosphorylation at the Active Site
Authors: Hurley, J.H. / Dean, A.M. / Sohl, J.L. / Koshland Junior, D.E. / Stroud, R.M.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase
Authors: Hurley, J.H. / Thorsness, P.E. / Ramalingam, V. / Helmers, N.H. / Koshland Junior, D.E. / Stroud, R.M.
History
DepositionJul 8, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)45,8101
Polymers45,8101
Non-polymers00
Water1,62190
1
A: ISOCITRATE DEHYDROGENASE

A: ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,6192
Polymers91,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5970 Å2
ΔGint-44 kcal/mol
Surface area32560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.500, 77.500, 92.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-550-

HOH

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Components

#1: Protein ISOCITRATE DEHYDROGENASE


Mass: 45809.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 mg/mlprotein1drop
2100 mM1dropNaCl
3100 mMHEPES1drop
40.05 MATP gamma S1drop
50.05 M1dropMgCl2
62 mMdithiothreitol1drop
70.01 %1dropNaN3
829-32 %PEG40001reservoir
910-90 mMammonium acetate1reservoir
102 mMdithiothreitol1reservoir
1150 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 13757 / % possible obs: 69 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Num. obs: 13753 / Num. measured all: 37773

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.42→7 Å / σ(F): 0
Details: CHARMM FORCE FIELD THR 104 - ARG 112 ARE POORLY DEFINED IN ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflection
Rfree0.23 --
Rwork0.181 --
obs0.181 11721 69 %
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.42→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 0 90 3269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPH11.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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