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- PDB-6lky: Crystal structure of isocitrate dehydrogenase from Methylococcus ... -

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Basic information

Entry
Database: PDB / ID: 6lky
TitleCrystal structure of isocitrate dehydrogenase from Methylococcus capsulatus
ComponentsPutative isocitrate dehydrogenase, NAD-dependent
KeywordsCARBOHYDRATE / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / tricarboxylic acid cycle / 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
ACETYL GROUP / ACETATE ION / CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative isocitrate dehydrogenase, NAD-dependent
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, S. / Wang, P. / Zhu, G.P.
CitationJournal: To Be Published
Title: Crystal structure of isocitrate dehydrogenase from Methylococcus capsulatus
Authors: Zhu, G.P.
History
DepositionDec 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative isocitrate dehydrogenase, NAD-dependent
B: Putative isocitrate dehydrogenase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,24313
Polymers73,1942
Non-polymers2,04911
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-57 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.168, 69.794, 71.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLYGLY(chain 'A' and (resid 2 through 14 or resid 16...AA2 - 132 - 13
12ILEILEGLYGLY(chain 'A' and (resid 2 through 14 or resid 16...AA16 - 6716 - 67
13THRTHRGLYGLY(chain 'A' and (resid 2 through 14 or resid 16...AA70 - 7670 - 76
14SERSERILEILE(chain 'A' and (resid 2 through 14 or resid 16...AA79 - 13079 - 130
15ASPASPALAALA(chain 'A' and (resid 2 through 14 or resid 16...AA133 - 208133 - 208
16METMETGLNGLN(chain 'A' and (resid 2 through 14 or resid 16...AA211 - 212211 - 212
17METMETILEILE(chain 'A' and (resid 2 through 14 or resid 16...AA215 - 252215 - 252
18ASPASPILEILE(chain 'A' and (resid 2 through 14 or resid 16...AA255 - 300255 - 300
19ALAALAARGARG(chain 'A' and (resid 2 through 14 or resid 16...AA303 - 338303 - 338
110NADNADNADNAD(chain 'A' and (resid 2 through 14 or resid 16...AC501
211HISHISGLYGLY(chain 'B' and (resid 2 through 14 or resid 16...BB2 - 132 - 13
212ILEILEGLYGLY(chain 'B' and (resid 2 through 14 or resid 16...BB16 - 6716 - 67
213THRTHRGLYGLY(chain 'B' and (resid 2 through 14 or resid 16...BB70 - 7670 - 76
214SERSERILEILE(chain 'B' and (resid 2 through 14 or resid 16...BB79 - 13079 - 130
215ASPASPALAALA(chain 'B' and (resid 2 through 14 or resid 16...BB133 - 208133 - 208
216METMETGLNGLN(chain 'B' and (resid 2 through 14 or resid 16...BB211 - 212211 - 212
217METMETILEILE(chain 'B' and (resid 2 through 14 or resid 16...BB215 - 252215 - 252
218ASPASPILEILE(chain 'B' and (resid 2 through 14 or resid 16...BB255 - 300255 - 300
219ALAALAARGARG(chain 'B' and (resid 2 through 14 or resid 16...BB303 - 338303 - 338
220NADNADNADNAD(chain 'B' and (resid 2 through 14 or resid 16...BH401

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative isocitrate dehydrogenase, NAD-dependent


Mass: 36596.852 Da / Num. of mol.: 2 / Mutation: F88L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: MCA3071 / Production host: Escherichia coli (E. coli) / References: UniProt: Q602J2

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Non-polymers , 5 types, 383 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 290 mM Calcium acetate monohydrate, 100 mM HEPES (pH 7.0), 10.8% (w/v) PEG 4000, 8% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43531 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 29.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.026 / Rsym value: 0.053 / Net I/σ(I): 30
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 9 / Num. unique obs: 4267 / CC1/2: 0.978 / Rpim(I) all: 0.11 / Rsym value: 0.281

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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: 5GRE

5gre


Resolution: 2.2→35.54 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7668
RfactorNum. reflection% reflection
Rfree0.2039 2057 4.89 %
Rwork0.1636 --
obs0.1655 42062 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 137 372 5623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00855425
X-RAY DIFFRACTIONf_angle_d1.35047368
X-RAY DIFFRACTIONf_chiral_restr0.0943870
X-RAY DIFFRACTIONf_plane_restr0.0075956
X-RAY DIFFRACTIONf_dihedral_angle_d8.75154494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.21161040.18652279X-RAY DIFFRACTION83.41
2.25-2.310.25511540.19482334X-RAY DIFFRACTION87.33
2.31-2.370.26351430.19372437X-RAY DIFFRACTION89.99
2.37-2.440.22141230.18442561X-RAY DIFFRACTION94.24
2.44-2.520.24361530.18312613X-RAY DIFFRACTION97.12
2.52-2.610.22481650.17662687X-RAY DIFFRACTION99.2
2.61-2.710.24891330.17242719X-RAY DIFFRACTION100
2.71-2.840.25371410.16972753X-RAY DIFFRACTION100
2.84-2.990.20081250.16412752X-RAY DIFFRACTION100
2.99-3.170.20921470.17042744X-RAY DIFFRACTION100
3.17-3.420.20731290.16432757X-RAY DIFFRACTION100
3.42-3.760.18671360.15022785X-RAY DIFFRACTION100
3.76-4.310.18321250.14372800X-RAY DIFFRACTION100
4.31-5.420.15631570.14212822X-RAY DIFFRACTION100
5.42-100.1971220.17412962X-RAY DIFFRACTION99.16

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