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- PDB-1bl5: ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCT... -

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Basic information

Entry
Database: PDB / ID: 1bl5
TitleISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 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 / 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
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsStoddard, B.L. / Cohen, B. / Brubaker, M. / Mesecar, A. / Koshland Junior, D.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs.
Authors: Stoddard, B.L. / Cohen, B.E. / Brubaker, M. / Mesecar, A.D. / 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 Junior, D.E. / Stroud, R.M.
#2: 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.
#3: 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.
#4: 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 23, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: 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 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4634
Polymers45,5491
Non-polymers9143
Water1,49583
1
A: ISOCITRATE DEHYDROGENASE
hetero molecules

A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9268
Polymers91,0992
Non-polymers1,8286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9190 Å2
ΔGint-56 kcal/mol
Surface area32220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.100, 106.100, 151.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ISOCITRATE DEHYDROGENASE / IDH


Mass: 45549.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RATE-LIMITED ENOLATE INTERMEDIATE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JLK1 / Gene: ICD / Variant: ICD(-) (DEFICIENT IN WT IDH GENE) / Plasmid: PTK513 / Gene (production host): ICD / 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 6

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 74 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.4 / Method: unknown
Details: Hurley, J.H., (1989) Proc.Nat.Acad.Sci.USA, 86, 8635.
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

DiffractionMean temperature: 274 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.7 / Wavelength: 0.7, 1.7
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
21.71
ReflectionResolution: 2.5→50 Å / Num. obs: 21751 / % possible obs: 90.8 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 7.5 / % possible all: 83.8
Reflection
*PLUS
Num. measured all: 360784

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
LaueViewdata reduction
LAUEGENdata reduction
LaueViewdata scaling
LAUEGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.5→50 Å / Rfactor Rfree error: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1372 5 %RANDOM
Rwork0.222 ---
obs0.222 27430 90.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 38 83 3317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.8
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

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