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- PDB-2d4v: Crystal structure of NAD dependent isocitrate dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 2d4v
TitleCrystal structure of NAD dependent isocitrate dehydrogenase from Acidithiobacillus thiooxidans
Componentsisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / alpha and beta protein / Isocitrate/Isopropylmalate dehydrogenase-like fold
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
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
CITRATE ANION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesAcidithiobacillus thiooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsImada, K. / Tamura, T. / Namba, K. / Inagaki, K.
CitationJournal: Proteins / Year: 2008
Title: Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity
Authors: Imada, K. / Tamura, T. / Takenaka, R. / Kobayashi, I. / Namba, K. / Inagaki, K.
History
DepositionOct 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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
B: isocitrate dehydrogenase
C: isocitrate dehydrogenase
D: isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,48112
Polymers185,0714
Non-polymers3,4108
Water24,0141333
1
A: isocitrate dehydrogenase
B: isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2416
Polymers92,5362
Non-polymers1,7054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-55 kcal/mol
Surface area30100 Å2
MethodPISA
2
C: isocitrate dehydrogenase
D: isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2416
Polymers92,5362
Non-polymers1,7054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-59 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.981, 125.981, 267.774
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


Mass: 46267.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus thiooxidans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8GAX0
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1333 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.6
Details: 0.95-1.05M sodium citrate, 10% glycerol, pH 4.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2003
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→57 Å / Num. all: 169211 / Num. obs: 157705 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.6
Reflection shellResolution: 1.9→2.03 Å / Redundancy: 12 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.837 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20264 7908 5 %RANDOM
Rwork0.17933 ---
all0.195 157462 --
obs0.18051 157462 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12943 0 228 1333 14504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02113439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9818255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.91231704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.658152345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.22040
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.37102
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.51560
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.358
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.538
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.671.58471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26213563
X-RAY DIFFRACTIONr_scbond_it2.27334968
X-RAY DIFFRACTIONr_scangle_it3.8414.54692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 358
Rwork0.183 7097

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