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- PDB-8i7e: Crystal structure of Glyceraldehyde 3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 8i7e
TitleCrystal structure of Glyceraldehyde 3-phosphate dehydrogenase from Salmonella typhi at 2.05A
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / 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
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKumar, N. / Dilawari, R. / Chaubey, G.K. / Modanwal, R. / Talukdar, S. / Dhiman, A. / Chaudhary, S. / Patidar, A. / Kumar, A. / Raje, C.I. ...Kumar, N. / Dilawari, R. / Chaubey, G.K. / Modanwal, R. / Talukdar, S. / Dhiman, A. / Chaudhary, S. / Patidar, A. / Kumar, A. / Raje, C.I. / Raje, M. / Kumaran, S.
Funding support India, 3items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
Indian Council of Medical Research India
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal structure of Glyceraldehyde 3-phosphate dehydrogenase from Salmonella typhi at 2.05A
Authors: Kumar, N. / Dilawari, R. / Chaubey, G.K. / Modanwal, R. / Talukdar, S. / Dhiman, A. / Chaudhary, S. / Patidar, A. / Kumar, A. / Raje, C.I. / Raje, M. / Kumaran, S.
History
DepositionJan 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 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


Theoretical massNumber of molelcules
Total (without water)71,2632
Polymers71,2632
Non-polymers00
Water3,441191
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)142,5264
Polymers142,5264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area15150 Å2
ΔGint-78 kcal/mol
Surface area43270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.901, 107.952, 122.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-474-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 35631.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: gapA_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4S3IK62
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M Imidazole pH 7.0, 40% PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 24, 2021
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.05→53.98 Å / Num. obs: 37312 / % possible obs: 97.81 % / Redundancy: 14.6 % / Biso Wilson estimate: 10.01 Å2 / CC1/2: 0.979 / Net I/σ(I): 1.68
Reflection shellResolution: 2.05→2.123 Å / Num. unique obs: 37312 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→53.98 Å / SU ML: 0.2975 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2914 1849 4.94 %
Rwork0.2444 35614 -
obs0.2467 37312 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→53.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 0 191 5111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234997
X-RAY DIFFRACTIONf_angle_d0.5496786
X-RAY DIFFRACTIONf_chiral_restr0.0446804
X-RAY DIFFRACTIONf_plane_restr0.0039880
X-RAY DIFFRACTIONf_dihedral_angle_d5.6261700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.47731490.43162632X-RAY DIFFRACTION95.24
2.1-2.160.36261280.32612680X-RAY DIFFRACTION96.3
2.16-2.230.38871270.34882671X-RAY DIFFRACTION96.38
2.23-2.310.50961350.39112688X-RAY DIFFRACTION96.68
2.31-2.410.28521290.26152703X-RAY DIFFRACTION97.19
2.41-2.520.24761490.23592727X-RAY DIFFRACTION97.49
2.52-2.650.27551410.22052681X-RAY DIFFRACTION97.65
2.65-2.810.24351660.22472739X-RAY DIFFRACTION98.18
2.82-3.030.2891560.24022720X-RAY DIFFRACTION98.49
3.03-3.340.24311330.19962795X-RAY DIFFRACTION98.72
3.34-3.820.24891400.20282795X-RAY DIFFRACTION99.16
3.82-4.810.20721400.15892834X-RAY DIFFRACTION99.5
4.81-53.980.22211560.17892949X-RAY DIFFRACTION99.65

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