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- PDB-6m3s: Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. ... -

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Basic information

Entry
Database: PDB / ID: 6m3s
TitleDimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase / CARBOHYDRATE
Function / homology
Function and homology information


isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
ISOCITRATE CALCIUM COMPLEX / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Isocitrate dehydrogenase
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, G.P.
CitationJournal: To Be Published
Title: Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004
Authors: Zhu, G.P.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1339
Polymers73,0672
Non-polymers2,0667
Water3,891216
1
B: Isocitrate dehydrogenase
hetero molecules

A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1339
Polymers73,0672
Non-polymers2,0667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/21
Buried area9580 Å2
ΔGint-57 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.735, 143.735, 65.289
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Isocitrate dehydrogenase / NAD-dependent isocitrate dehydrogenase


Mass: 36533.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: D0A35_19175, TR80_00940, XcmpCFBP7700_13825 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S4JWD6, isocitrate dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ICA / ISOCITRATE CALCIUM COMPLEX


Mass: 231.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7CaO7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 4 mM DL-Isocitrate, 4 mM NAD, 2 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34265 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 37.13 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.058 / Net I/σ(I): 22.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.44 / Num. unique obs: 1733 / R split: 0.21 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRH

5grh


Resolution: 2.3→48.33 Å / SU ML: 0.2459 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.5784
RfactorNum. reflection% reflection
Rfree0.2248 1995 5.83 %
Rwork0.1746 --
obs0.1775 34244 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 134 216 5343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415257
X-RAY DIFFRACTIONf_angle_d1.78817139
X-RAY DIFFRACTIONf_chiral_restr0.086843
X-RAY DIFFRACTIONf_plane_restr0.0072927
X-RAY DIFFRACTIONf_dihedral_angle_d21.79931945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.26161410.22352261X-RAY DIFFRACTION97.68
2.35-2.420.27131440.22072294X-RAY DIFFRACTION99.71
2.42-2.490.27871440.21992300X-RAY DIFFRACTION99.39
2.49-2.570.25591370.20012281X-RAY DIFFRACTION99.63
2.57-2.660.26221490.19792314X-RAY DIFFRACTION99.56
2.66-2.770.25691380.19942297X-RAY DIFFRACTION99.23
2.77-2.890.28341440.20652303X-RAY DIFFRACTION99.27
2.89-3.040.27021420.19262292X-RAY DIFFRACTION99.27
3.04-3.240.25541420.19632312X-RAY DIFFRACTION99.23
3.24-3.490.25641410.19282288X-RAY DIFFRACTION98.94
3.49-3.840.21041410.17462315X-RAY DIFFRACTION98.75
3.84-4.390.21061440.15322309X-RAY DIFFRACTION98.75
4.39-5.530.17611400.13332330X-RAY DIFFRACTION99
5.53-100.1681480.14732353X-RAY DIFFRACTION97.73

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