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- PDB-5z16: A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5z16
TitleA novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase / TCA cycle / glyoxylate bypass / pathogenesis
Function / homologyIsocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / PHOSPHATE ION / Isocitrate dehydrogenase [NADP]
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSong, P. / Huang, S.P. / Wang, P. / Zhu, G.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570010, 31170005, 31400003 China
CitationJournal: To Be Published
Title: A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii
Authors: Wang, P. / Zhu, G.P. / Song, P. / Huang, S.P.
History
DepositionDec 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)167,4436
Polymers167,2052
Non-polymers2394
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-30 kcal/mol
Surface area58970 Å2
Unit cell
Length a, b, c (Å)137.161, 137.161, 238.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Isocitrate dehydrogenase / Isocitrate dehydrogenase (NADP(+)) / Isocitrate dehydrogenase [NADP] / Isocitrate dehydrogenase / ...Isocitrate dehydrogenase (NADP(+)) / Isocitrate dehydrogenase [NADP] / Isocitrate dehydrogenase / NADP-dependent


Mass: 83602.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: icd_2, A7M79_07490, A7N09_00330, APD06_04285, APD31_03935, AZE33_14960, B4R90_02155, B9X91_18100, B9X95_15090, BGC29_03310, BWP00_11420, CAS83_18605, CAT78_13885, CEJ63_01165, CHH39_15940, ...Gene: icd_2, A7M79_07490, A7N09_00330, APD06_04285, APD31_03935, AZE33_14960, B4R90_02155, B9X91_18100, B9X95_15090, BGC29_03310, BWP00_11420, CAS83_18605, CAT78_13885, CEJ63_01165, CHH39_15940, CHQ89_08020, IX87_09060, LV38_02052
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: V5VCI0, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG 4000, 14% 2-propanol, 40mM MgCl2, 20% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 46423 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 3.2
Reflection shellResolution: 3→8.13 Å / Rmerge(I) obs: 0.402 / Num. unique obs: 2297

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBC

3mbc


Resolution: 3→48.537 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.16
RfactorNum. reflection% reflection
Rfree0.2758 2266 4.9 %
Rwork0.2047 --
obs0.2082 46269 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→48.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11408 0 12 369 11789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111637
X-RAY DIFFRACTIONf_angle_d1.60815747
X-RAY DIFFRACTIONf_dihedral_angle_d16.8744355
X-RAY DIFFRACTIONf_chiral_restr0.0581761
X-RAY DIFFRACTIONf_plane_restr0.0082043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9997-3.06490.32371370.24452703X-RAY DIFFRACTION100
3.0649-3.13620.33721350.26552730X-RAY DIFFRACTION100
3.1362-3.21460.40251370.26672679X-RAY DIFFRACTION100
3.2146-3.30150.33511420.2462709X-RAY DIFFRACTION100
3.3015-3.39870.28391390.23452702X-RAY DIFFRACTION100
3.3987-3.50830.29941560.22822697X-RAY DIFFRACTION100
3.5083-3.63370.30721470.22082716X-RAY DIFFRACTION100
3.6337-3.77910.30351360.21362714X-RAY DIFFRACTION100
3.7791-3.9510.29341660.19622702X-RAY DIFFRACTION100
3.951-4.15920.22971390.18072757X-RAY DIFFRACTION100
4.1592-4.41970.27171370.16972742X-RAY DIFFRACTION100
4.4197-4.76060.25591330.16062750X-RAY DIFFRACTION100
4.7606-5.23920.24251440.17172763X-RAY DIFFRACTION100
5.2392-5.99620.25341250.19752818X-RAY DIFFRACTION100
5.9962-7.54990.28811640.21922809X-RAY DIFFRACTION100
7.5499-48.5430.21521290.20423012X-RAY DIFFRACTION99

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