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- PDB-8ihe: Rv1122(gnd2) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8ihe
TitleRv1122(gnd2) in Mycobacterium tuberculosis
ComponentsProbable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2
KeywordsHYDROLASE / dehydrogenase / tetramer
Function / homology
Function and homology information


organic acid catabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / D-gluconate metabolic process / pentose-phosphate shunt / NADP binding / plasma membrane
Similarity search - Function
6-phosphogluconate dehydrogenase, YqeC-type / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsChen, Y.J. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670737 China
CitationJournal: To Be Published
Title: Rv1122(gnd2) in Mycobacterium tuberculosis
Authors: Chen, Y.J. / Su, D.
History
DepositionFeb 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2
B: Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2
C: Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2
D: Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2


Theoretical massNumber of molelcules
Total (without water)145,6004
Polymers145,6004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29930 Å2
ΔGint-207 kcal/mol
Surface area44740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.991, 107.246, 137.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2


Mass: 36400.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: gnd2, Rv1122 / Production host: Escherichia coli (E. coli) / References: UniProt: O06574

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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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% PEG5000 0.2M ammonium sulphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 37669 / % possible obs: 99.1 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 7
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.972 / Num. unique obs: 1839

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→26.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.483 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30746 1842 4.9 %RANDOM
Rwork0.21623 ---
obs0.2206 35694 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0 Å2
2---0.19 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.74→26.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9862 0 0 0 9862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310057
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179478
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.63813628
X-RAY DIFFRACTIONr_angle_other_deg1.2181.58121762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7951304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41320.721541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.377151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5171596
X-RAY DIFFRACTIONr_chiral_restr0.0650.21279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211615
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.3757.6785240
X-RAY DIFFRACTIONr_mcbond_other7.3757.6775239
X-RAY DIFFRACTIONr_mcangle_it11.36211.496536
X-RAY DIFFRACTIONr_mcangle_other11.36211.496537
X-RAY DIFFRACTIONr_scbond_it6.6698.0754817
X-RAY DIFFRACTIONr_scbond_other6.6688.0754818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.3711.9517093
X-RAY DIFFRACTIONr_long_range_B_refined15.31289.52211242
X-RAY DIFFRACTIONr_long_range_B_other15.31189.51911243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 122 -
Rwork0.329 2430 -
obs--92.67 %

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