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- PDB-4icd: REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVE... -

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Basic information

Entry
Database: PDB / ID: 4icd
TitleREGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVES NO LONG-RANGE CONFORMATIONAL CHANGE IN THE FREE ENZYME
ComponentsPHOSPHORYLATED ISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (NAD(A)-CHOH(D))
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 / cytoplasm / cytosol
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: 2.5 Å
AuthorsHurley, J.H. / Dean, A.M. / Thorsness, P.E. / Koshlandjunior, D.E. / Stroud, R.M.
Citation
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 Jr., D.E. / Stroud, R.M.
#1: 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. / Koshlandjunior, 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. / Koshlandjunior, D.E. / Stroud, R.M.
History
DepositionDec 28, 1989Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHORYLATED ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)45,8901
Polymers45,8901
Non-polymers00
Water2,576143
1
A: PHOSPHORYLATED ISOCITRATE DEHYDROGENASE

A: PHOSPHORYLATED ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,7792
Polymers91,7792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6450 Å2
ΔGint-55 kcal/mol
Surface area30730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.100, 105.100, 150.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE SER 113 IS A PHOSPHORYLATED SERINE. / 2: PRO 262 IS A CIS PROLINE.

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Components

#1: Protein PHOSPHORYLATED ISOCITRATE DEHYDROGENASE


Mass: 45889.543 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.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.8 %
Crystal grow
*PLUS
pH: 5.4 / Method: unknown / Details: took J. H. Hurley et al.,from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 mg/mlprotein11
230 %satammonium sulfate11
3100 mM11NaCl
435 mM11Na2HPO4
59 mMcitric acid11
60.2 mMdithiothreitol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 21162 / Observed criterion σ(F): 1 / Num. measured all: 156365 / Rmerge F obs: 0.121

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.169 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 143 3293
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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