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- PDB-2i5p: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase iso... -

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Basic information

Entry
Database: PDB / ID: 2i5p
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase isoform 1 from K. marxianus
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / Rossmann fold / apo form / dimer / GAPDH
Function / homology
Function and homology information


external encapsulating structure / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / alpha-D-glucopyranose / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFerreira-da-Silva, F. / Pereira, P.J.B. / Gales, L. / Moradas-Ferreira, P. / Damas, A.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Crystal and Solution Structures of Glyceraldehyde-3-phosphate Dehydrogenase Reveal Different Quaternary Structures.
Authors: Ferreira-da-Silva, F. / Pereira, P.J. / Gales, L. / Roessle, M. / Svergun, D.I. / Moradas-Ferreira, P. / Damas, A.M.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 15, 2020Group: Advisory / Data collection / Database references
Category: chem_comp / pdbx_unobs_or_zero_occ_atoms ...chem_comp / pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell / struct_ref_seq_dif
Item: _chem_comp.type / _reflns.pdbx_Rmerge_I_obs ..._chem_comp.type / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2336
Polymers73,7162
Non-polymers5174
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-32 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.900, 70.900, 358.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11O-2101-

HOH

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Components

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


Mass: 36857.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Strain: ATCC10022 / Gene: GAP1 / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P84998, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 287 K / pH: 7.5
Details: 7% PEG6000, 4% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→65.9 Å / Num. obs: 42054 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAD

1gad


Resolution: 2.3→65.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2743821.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2125 5.1 %RANDOM
Rwork0.216 ---
obs0.216 42054 99.9 %-
all-42106 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8769 Å2 / ksol: 0.361572 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.25 Å20 Å20 Å2
2--10.25 Å20 Å2
3----20.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→65.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 30 230 4922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.832.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 348 5.1 %
Rwork0.267 6526 -
obs--100 %

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