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- PDB-8hmn: Crystal structure of GAPDH complexed with arsenate from Lactiplan... -

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Basic information

Entry
Database: PDB / ID: 8hmn
TitleCrystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / arsenate / Lactiplantibacillus plantarum
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ARSENATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsYoneda, K. / Kinoshita, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K21259 Japan
CitationJournal: To Be Published
Title: Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum
Authors: Yoneda, K. / Kinoshita, H.
History
DepositionDec 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,16917
Polymers154,5894
Non-polymers3,58013
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The structure of 6IQM is also a homotetramer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22360 Å2
ΔGint-90 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.850, 123.964, 132.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38647.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: gap / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q88YH6

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Non-polymers , 5 types, 850 molecules

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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AsO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25%(w/v) PEG 1500, 0.1 M MIB buffer

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→48.49 Å / Num. obs: 69658 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Χ2: 1.12 / Net I/σ(I): 13.1
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5267 / CC1/2: 0.762 / Rpim(I) all: 0.574 / Χ2: 0.96 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→45.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.931 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 3572 5.1 %RANDOM
Rwork0.21606 ---
obs0.21835 65890 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0 Å2
2---0.51 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.16→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9950 0 220 837 11007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310591
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179984
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.64314409
X-RAY DIFFRACTIONr_angle_other_deg1.2821.58322956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87851347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70523.551490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.723151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6191548
X-RAY DIFFRACTIONr_chiral_restr0.0660.21477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022315
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_it2.5813.3085407
X-RAY DIFFRACTIONr_mcbond_other2.5813.3085406
X-RAY DIFFRACTIONr_mcangle_it3.9564.9466747
X-RAY DIFFRACTIONr_mcangle_other3.9554.9466748
X-RAY DIFFRACTIONr_scbond_it2.6423.535184
X-RAY DIFFRACTIONr_scbond_other2.6423.535185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0865.1897663
X-RAY DIFFRACTIONr_long_range_B_refined13.46443.26412640
X-RAY DIFFRACTIONr_long_range_B_other13.3743.00812490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A106060.05
12B106060.05
21A106080.05
22C106080.05
31A104840.07
32D104840.07
41B105800.06
42C105800.06
51B104740.07
52D104740.07
61C107260.07
62D107260.07
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 278 -
Rwork0.272 4829 -
obs--99.88 %

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