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

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Basic information

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


isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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
BENZOIC ACID / Isocitrate dehydrogenase / Isocitrate dehydrogenase
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsZhu, G.P.
CitationJournal: To Be Published
Title: Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004
Authors: Zhu, G.P.
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6392
Polymers35,5171
Non-polymers1221
Water6,972387
1
A: Isocitrate dehydrogenase
hetero molecules

A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2774
Polymers71,0332
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area4250 Å2
ΔGint-16 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.052, 156.657, 68.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 35516.504 Da / Num. of mol.: 1
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, UniProt: A0A0H2XBX7*PLUS, isocitrate dehydrogenase (NAD+)
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5,0.2 M LiSO4, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 1.6→50 Å / Num. obs: 40051 / % possible obs: 96 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.08 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.047 / Net I/σ(I): 24.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3 / Num. unique obs: 1993 / CC1/2: 0.814 / Rpim(I) all: 0.255 / % possible all: 98.3

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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: 1.61→43.42 Å / SU ML: 0.1583 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 21.0084
RfactorNum. reflection% reflection
Rfree0.2116 1941 4.98 %
Rwork0.1896 --
obs0.1907 39015 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.78 Å2
Refinement stepCycle: LAST / Resolution: 1.61→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 9 388 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782576
X-RAY DIFFRACTIONf_angle_d0.95343499
X-RAY DIFFRACTIONf_chiral_restr0.0606416
X-RAY DIFFRACTIONf_plane_restr0.0062461
X-RAY DIFFRACTIONf_dihedral_angle_d3.31822126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.24891040.22811910X-RAY DIFFRACTION67.4
1.65-1.690.24411380.23112599X-RAY DIFFRACTION90.87
1.69-1.740.26561320.23552616X-RAY DIFFRACTION91.91
1.74-1.80.30171360.23122648X-RAY DIFFRACTION93.14
1.8-1.860.261370.22632725X-RAY DIFFRACTION94.3
1.86-1.940.25591420.21422695X-RAY DIFFRACTION95.07
1.94-2.030.22911430.20782700X-RAY DIFFRACTION94.99
2.03-2.130.25341440.20392727X-RAY DIFFRACTION95.29
2.13-2.270.24071440.19062775X-RAY DIFFRACTION96.02
2.27-2.440.20581450.18862727X-RAY DIFFRACTION95.61
2.44-2.690.20191440.19372750X-RAY DIFFRACTION95.13
2.69-3.080.22851450.19042746X-RAY DIFFRACTION94.42
3.08-3.880.16921430.16772719X-RAY DIFFRACTION92.71
3.88-43.420.16751440.1592737X-RAY DIFFRACTION89.42

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