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- PDB-1pb3: Sites of binding and orientation in a four location model for pro... -

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Basic information

Entry
Database: PDB / ID: 1pb3
TitleSites of binding and orientation in a four location model for protein stereospecificity.
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / isocitrate dehydrogense / IDH / stereospecificity / entantiomer
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMesecar, A.D. / Koshland Jr., D.E.
Citation
Journal: IUBMB Life / Year: 2000
Title: Sites of Binding and Orientation in a Four-Location Model for Protein Stereospecificity.
Authors: Mesecar, A.D. / Koshland Jr., D.E.
#1: Journal: Nature / Year: 2000
Title: Structural Biology: A New Model for Protein Stereospecificity.
Authors: Mesecar, A.D. / Koshland Jr., D.E.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2786
Polymers45,8101
Non-polymers4685
Water5,116284
1
A: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55612
Polymers91,6192
Non-polymers93710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8760 Å2
ΔGint-117 kcal/mol
Surface area31030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.669, 103.669, 150.124
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 [NADP] / Oxalosuccinate decarboxylase / IDH / NADP+-specific ICDH / IDP


Mass: 45809.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: wildtype / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ICD OR ICDA OR ICDE OR B1136 / Production host: Escherichia coli (E. coli)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was ...Details: IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140 mg/mlprotein1drop
235 mM1reservoirNa2HPO4
39 mMcitric acid1reservoir
4100 mM1reservoirNaCl
50.2 mMdithiothreitol1reservoirpH5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 90369 / Num. obs: 88368 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 32
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.8 / % possible all: 100
Reflection
*PLUS
Num. obs: 90256 / % possible obs: 99.9 % / Num. measured all: 1751210

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.93 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 8832 10 %RANDOM
Rwork0.194 ---
all0.194 90369 --
obs0.194 88368 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.1591 Å2 / ksol: 0.400861 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 28 284 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 823 9.8 %
Rwork0.264 7570 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ALL.PARALL.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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