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- PDB-6icd: REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE -

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Basic information

Entry
Database: PDB / ID: 6icd
TitleREGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (NAD(A)-CHOH(D))
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
Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsHurley, J.H. / Dean, A.M. / Sohl, J.L. / Koshlandjunior, D.E. / Stroud, R.M.
Citation
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, 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. / 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.
#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. / Koshlandjunior, D.E. / Stroud, R.M.
History
DepositionMay 30, 1990Processing site: BNL
Revision 1.0Oct 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 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)45,8381
Polymers45,8381
Non-polymers00
Water181
1
A: ISOCITRATE DEHYDROGENASE

A: ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,6752
Polymers91,6752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6380 Å2
ΔGint-51 kcal/mol
Surface area30930 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 PRO 262 IS A CIS PROLINE.

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Components

#1: Protein ISOCITRATE DEHYDROGENASE /


Mass: 45837.574 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 / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.53 Å3/Da / Density % sol: 72.82 %
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
234 %satammonium sulfate11
3100 mM11Nacl
435 mM11Na2HPO4
59 mMcitric acid11
60.2 mMdithiothreitol11

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. all: 21721 / Num. obs: 20711 / % possible obs: 79.5 % / Observed criterion σ(F): 1 / Num. measured all: 89070 / Rmerge F obs: 0.204

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.163 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 0 1 3150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.3
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
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 1 / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d3.3

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