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- PDB-7y1u: Crystal structure of isocitrate dehydrogenase from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 7y1u
TitleCrystal structure of isocitrate dehydrogenase from Campylobacter corcagiensis
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Complex / NADP+ / Mn2+ / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / nucleotide binding / metal ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesCampylobacter corcagiensis (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBian, M.J. / Cheng, Q.P. / Wang, P. / Zhu, G.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of isocitrate dehydrogenase from Campylobacter corcagiensis
Authors: Bian, M.J. / Cheng, Q.P. / Wang, P. / Zhu, G.P.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,00713
Polymers81,1541
Non-polymers1,85312
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.501, 92.694, 147.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isocitrate dehydrogenase [NADP] / Oxalosuccinate decarboxylase


Mass: 81153.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter corcagiensis (Campylobacter)
Gene: IMC76_08370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7M1LFL5, isocitrate dehydrogenase (NADP+)

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Non-polymers , 6 types, 161 molecules

#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Li2SO4, 0.1 M Tris pH8.5, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18067 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18067 Å / Relative weight: 1
ReflectionResolution: 2.5→49.11 Å / Num. obs: 30370 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Net I/σ(I): 18.3
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3368 / CC1/2: 0.856 / Rpim(I) all: 0.272

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITW

1itw


Resolution: 2.5→48.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.462 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.532 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1548 5.1 %RANDOM
Rwork0.1882 ---
obs0.1919 28767 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.21 Å2 / Biso mean: 46.011 Å2 / Biso min: 20.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å2-0 Å2
2---1.58 Å20 Å2
3---3.76 Å2
Refinement stepCycle: final / Resolution: 2.5→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 112 149 5967
Biso mean--48.79 38.3 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135926
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175631
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.6567984
X-RAY DIFFRACTIONr_angle_other_deg1.2571.59813135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89224.24283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.762151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5871523
X-RAY DIFFRACTIONr_chiral_restr0.0790.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021122
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 107 -
Rwork0.265 2074 -
all-2181 -
obs--100 %

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