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- PDB-7d1g: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase GAP... -

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Basic information

Entry
Database: PDB / ID: 7d1g
TitleCrystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase GAPDH from Clostridium beijerinckii
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glyceraldehyde-3-Phosphate Dehydrogenase GAPDH / Clostridium beijerinckii
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
BETA-MERCAPTOETHANOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii NCIMB 8052 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsChen, Y. / Lan, J. / Liu, W. / Wang, L. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31200556 China
National Natural Science Foundation of China (NSFC)21272031 China
CitationJournal: To Be Published
Title: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase GAPDH from Clostridium beijerinckii
Authors: Chen, Y. / Lan, J. / Liu, W. / Wang, L. / Xu, Y.
History
DepositionSep 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0273
Polymers35,9251
Non-polymers1022
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.640, 120.640, 122.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 35924.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii NCIMB 8052 (bacteria)
Strain: NCIMB 8052 / Gene: Cbei_0597 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: A6LR04, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium pH 8.5 0.2 M Magnesium chloride hexahydrate 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 71898 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 23.58 Å2 / Rsym value: 0.145 / Net I/σ(I): 34.22
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 2218 / Rsym value: 0.839

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→42.91 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 3588 5 %
Rwork0.1931 68216 -
obs0.194 71804 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.84 Å2
Refinement stepCycle: LAST / Resolution: 1.58→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 5 368 2864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812536
X-RAY DIFFRACTIONf_angle_d0.923437
X-RAY DIFFRACTIONf_chiral_restr0.0554407
X-RAY DIFFRACTIONf_plane_restr0.0053445
X-RAY DIFFRACTIONf_dihedral_angle_d7.35162090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.3111350.26962316X-RAY DIFFRACTION90.18
1.6-1.620.2981460.27222608X-RAY DIFFRACTION100
1.62-1.640.28881130.26842586X-RAY DIFFRACTION100
1.64-1.670.27291280.25242627X-RAY DIFFRACTION99.96
1.67-1.70.2641370.25172587X-RAY DIFFRACTION100
1.7-1.720.26631410.23972599X-RAY DIFFRACTION99.96
1.72-1.750.30011440.23342595X-RAY DIFFRACTION100
1.75-1.780.26161290.22882580X-RAY DIFFRACTION100
1.82-1.860.23871340.22862601X-RAY DIFFRACTION99.96
1.86-1.90.24631410.22412591X-RAY DIFFRACTION100
1.9-1.940.24781370.21182619X-RAY DIFFRACTION100
1.94-1.990.20771590.20482590X-RAY DIFFRACTION100
1.99-2.040.21991420.20472609X-RAY DIFFRACTION100
2.04-2.10.25121320.20172624X-RAY DIFFRACTION100
2.17-2.250.19621290.19092641X-RAY DIFFRACTION99.96
2.34-2.440.24281330.192643X-RAY DIFFRACTION100
2.44-2.570.23951460.20082652X-RAY DIFFRACTION100
2.57-2.730.22431320.1952658X-RAY DIFFRACTION100
2.73-2.950.25381400.20152656X-RAY DIFFRACTION100
3.24-3.710.19261550.17972681X-RAY DIFFRACTION99.82

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