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- PDB-8de5: Structure of glyceraldehyde-3-phosphate dehydrogenase from Paraco... -

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Basic information

Entry
Database: PDB / ID: 8de5
TitleStructure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glyceraldehyde-3-Phosphate Dehydrogenase / Paracoccidioides lutzii / Paracoccidioidomycosis / Aldonic Sugar Acid
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 / cytoplasm
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
D-galactonic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesParacoccidioides lutzii Pb01 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHernandez-Prieto, J.H. / Martini, V.P. / Iulek, J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other government Brazil
CitationJournal: Biochimie / Year: 2023
Title: Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid.
Authors: Hernandez-Prieto, J.H. / Martini, V.P. / Iulek, J.
History
DepositionJun 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)38,05710
Polymers36,5481
Non-polymers1,5089
Water7,458414
1
A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,22640
Polymers146,1934
Non-polymers6,03336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation10_545-x,-y-1,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area25320 Å2
ΔGint-200 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.713, 118.713, 158.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21A-898-

HOH

31A-911-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36548.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccidioides lutzii Pb01 (fungus) / Strain: ATCC MYA-826 / Pb01 / Gene: GPD, PAAG_08468 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8X1X3, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-J0M / D-galactonic acid / D-galactonate


Mass: 196.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 3.67 Å3/Da / Density % sol: 66.5 % / Description: Tetragonal trapezohedral
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 0.2 M ammonium sulfate, 25.5% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.02→83.94 Å / Num. obs: 37329 / % possible obs: 100 % / Redundancy: 56.6 % / Biso Wilson estimate: 35.362 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.606 / Rpim(I) all: 0.074 / Rrim(I) all: 0.611 / Net I/σ(I): 10.4
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 26.6 % / Rmerge(I) obs: 3.767 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1814 / CC1/2: 0.372 / Rpim(I) all: 0.742 / Rrim(I) all: 3.84 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS2.2.11-gad03a188b-releasedata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7U4S

7u4s


Resolution: 2.02→83.94 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1936 5.21 %Random selection
Rwork0.1648 35203 --
obs0.1665 37139 99.54 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.41 Å2
Refinement stepCycle: LAST / Resolution: 2.02→83.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 98 414 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262731
X-RAY DIFFRACTIONf_angle_d0.56683707
X-RAY DIFFRACTIONf_chiral_restr0.0469423
X-RAY DIFFRACTIONf_plane_restr0.0048468
X-RAY DIFFRACTIONf_dihedral_angle_d11.2398997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.40141050.32592469X-RAY DIFFRACTION99.31
2.07-2.130.30711360.31222490X-RAY DIFFRACTION99.7
2.13-2.190.30111280.26032474X-RAY DIFFRACTION99.09
2.19-2.260.28881430.24362483X-RAY DIFFRACTION99.28
2.26-2.340.25341380.23232459X-RAY DIFFRACTION99.12
2.34-2.430.24341370.20512477X-RAY DIFFRACTION99.39
2.43-2.540.24851680.20152494X-RAY DIFFRACTION99.59
2.55-2.680.26391640.20272454X-RAY DIFFRACTION99.35
2.68-2.850.18731630.18962460X-RAY DIFFRACTION99.47
2.85-3.070.18811440.15142516X-RAY DIFFRACTION99.89
3.07-3.380.17721220.142554X-RAY DIFFRACTION99.74
3.38-3.860.1731080.13352580X-RAY DIFFRACTION99.74
3.87-4.870.14371410.1132571X-RAY DIFFRACTION99.89
4.87-83.940.16091390.14582722X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 0.677084236769 Å / Origin y: -39.9064479659 Å / Origin z: -24.9261160368 Å
111213212223313233
T0.337340252598 Å20.0699893829886 Å20.00967232545485 Å2-0.31480589726 Å2-0.087588644874 Å2--0.289604130193 Å2
L1.43327444678 °20.911943058606 °20.190300488273 °2-1.77639309556 °20.0982310635953 °2--1.15770807968 °2
S0.062300777178 Å °-0.302768669069 Å °0.426224541774 Å °0.24528468858 Å °-0.165861359954 Å °0.416075678551 Å °-0.170191293332 Å °-0.146765776608 Å °0.0299196251534 Å °
Refinement TLS groupSelection details: chain A

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