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- PDB-1ai3: ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTU... -

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Basic information

Entry
Database: PDB / ID: 1ai3
TitleORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / NADP / PHOSPHORYLATION / GLYOXYLATE BYPASS
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
ISOCITRIC ACID / Chem-NDO / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStoddard, B.L. / Mesecar, A. / Koshland Junior, D.E.
Citation
Journal: Science / Year: 1997
Title: Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.
Authors: Mesecar, A.D. / Stoddard, B.L. / Koshland Jr., D.E.
#1: Journal: Biochemistry / Year: 1996
Title: Determinants of Cofactor Specificity in Isocitrate Dehydrogenase: Structure of an Engineered Nadp+--> Nad+ Specificity-Reversal Mutant
Authors: Hurley, J.H. / Chen, R. / Dean, A.M.
#2: Journal: Biochemistry / Year: 1993
Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Dinucleotide Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex
Authors: Stoddard, B.L. / Dean, A. / Koshland Junior, D.E.
History
DepositionApr 30, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 2, 2011Group: Non-polymer description
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn / struct_conn_type

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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)46,7704
Polymers45,8101
Non-polymers9613
Water5,368298
1
A: ISOCITRATE DEHYDROGENASE
hetero molecules

A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5418
Polymers91,6192
Non-polymers1,9226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9670 Å2
ΔGint-51 kcal/mol
Surface area30940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.400, 102.400, 150.700
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 / OXALOSUCCINATE DECARBOXYLASE / IDH


Mass: 45809.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: DEK2004 / Plasmid: PICD / Production host: Escherichia coli (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NDO / NICOTINAMIDE-(6-DEAMINO-6-HYDROXY-ADENINE)-DINUCLEOTIDE PHOSPHATE


Mass: 744.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N6O18P3
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.31 Å3/Da / Density % sol: 71.46 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 5.4 / Method: unknown
Details: Hurley, J.H., (1989) Proc. Natl. Acad. Sci. U.S.A., 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 / Details: TORROIDAL MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 62143 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.18 / % possible all: 94
Reflection
*PLUS
Num. measured all: 198342 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ISO

1iso


Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3107 5 %RANDOM
Rwork0.188 ---
obs0.188 62143 97.2 %-
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 62 298 3556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
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 DIFFRACTION1PARAM20X.PROTOPH20X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17

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