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- PDB-7jh0: Crystallographic structure of glyceraldehyde-3-phosphate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 7jh0
TitleCrystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Schistosoma mansoni
Components(Glyceraldehyde-3-phosphate ...Glyceraldehyde 3-phosphate) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsBoreiko, S. / Silva, M. / Iulek, J.
CitationJournal: Biochimie / Year: 2021
Title: Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth.
Authors: Boreiko, S. / Silva, M. / Iulek, J.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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: 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)146,72511
Polymers145,9664
Non-polymers7597
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint-77 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.123, 80.123, 417.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Glyceraldehyde-3-phosphate ... , 2 types, 4 molecules ABCD

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH / Major larval surface antigen / P-37


Mass: 36503.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH / Major larval surface antigen / P-37


Mass: 36455.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 5 types, 210 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% ...Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% Mix of precipitants (20% V/V Glicerol e 10% w/V PEG 40,000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.08
ReflectionResolution: 2.51→57.76 Å / Num. obs: 51375 / % possible obs: 99.9 % / Redundancy: 21.57 % / CC1/2: 0.999 / Rrim(I) all: 0.172 / Net I/σ(I): 14.35
Reflection shellResolution: 2.51→2.57 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3515 / CC1/2: 0.501 / Rrim(I) all: 2.654 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
XDS3.25data processing
PHENIXmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K9D

4k9d


Resolution: 2.51→57.76 Å / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 35.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2726 1968 3.83 %
Rwork0.2132 49363 -
obs0.2158 51375 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.41 Å2 / Biso mean: 74.0242 Å2 / Biso min: 35.66 Å2
Refinement stepCycle: final / Resolution: 2.51→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 50 203 10172
Biso mean--82.25 57.37 -
Num. residues----1352
LS refinement shellResolution: 2.51→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3314 139 -
Rwork0.3378 3523 -
all-3662 -
obs--96 %
Refinement TLS params.Method: refined / Origin x: -8.9134 Å / Origin y: 11.2973 Å / Origin z: -3.4192 Å
111213212223313233
T0.44 Å2-0.0994 Å2-0.0984 Å2-0.3196 Å2-0.0018 Å2--0.7127 Å2
L1.0325 °2-0.3296 °20.3037 °2-0.6516 °2-0.1299 °2--1.2204 °2
S-0.1876 Å °0.1113 Å °0.2704 Å °0.1141 Å °0.0208 Å °-0.018 Å °-0.0785 Å °-0.0509 Å °0.1083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain DA1 - 338
2X-RAY DIFFRACTION1chain A or chain B or chain C or chain DB1 - 338
3X-RAY DIFFRACTION1chain A or chain B or chain C or chain DC1 - 338
4X-RAY DIFFRACTION1chain A or chain B or chain C or chain DD1 - 338

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