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- PDB-2vyn: Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer -

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Basic information

Entry
Database: PDB / ID: 2vyn
TitleStructure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer
Components(GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEGlyceraldehyde 3-phosphate dehydrogenase) x 2
KeywordsOXIDOREDUCTASE / GAPDH / CONTRACEPTIVE / RAT SPERM / GLYCERALDEHYDE-3-PHOSPHATE / ALPHA CHLOROHYDRIN
Function / homology
Function and homology information


Glycolysis / sperm fibrous sheath / sperm principal piece / Gluconeogenesis / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / spermatid development / acrosomal vesicle ...Glycolysis / sperm fibrous sheath / sperm principal piece / Gluconeogenesis / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / spermatid development / acrosomal vesicle / glycolytic process / cilium / glucose metabolic process / NAD binding / NADP binding / membrane / identical protein 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
FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase A / Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFrayne, J. / Taylor, A. / Hall, L. / Hadfield, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of Insoluble Rat Sperm Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) Via Heterotetramer Formation with Escherichia Coli Gapdh Reveals Target for Contraceptive Design.
Authors: Frayne, J. / Taylor, A. / Cameron, G. / Hadfield, A.T.
History
DepositionJul 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 31, 2018Group: Data collection / Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific ..._entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.pdbx_variant / _entity_src_nat.strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)146,59922
Polymers143,3014
Non-polymers3,29818
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17620 Å2
ΔGint-133 kcal/mol
Surface area54550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)68.445, 103.562, 177.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.894, 0.435, 0.112), (0.434, -0.9, 0.027), (0.113, 0.025, -0.993)-22.2399, 86.23087, 40.96305
2given(-0.9964, 0.01771, -0.08294), (-0.0032, -0.98511, -0.17187), (-0.08475, -0.17099, 0.98162)46.85013, 105.05235, 11.08776

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Components

#1: Protein GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 35641.434 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant: pLysS
References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Protein GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 36376.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 102-432 / Source method: isolated from a natural source / Details: DNA WAS EXTRACTED DIRECTLY FROM RAT TESTIS / Source: (natural) RATTUS NORVEGICUS (Norway rat) / Tissue: TESTISTesticle
References: UniProt: Q9ESV6, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2M NA FORMATE, 20% PEG 3350, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 63912 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAD

1gad


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.298 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3224 5.1 %RANDOM
Rwork0.157 ---
obs0.16 60321 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10026 0 218 844 11088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210555
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.97914337
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18251353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57824.753425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.527151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9411552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21659
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.25444
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27214
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21061
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.38936831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21510695
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.41964204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.989103634
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 244
Rwork0.164 4412

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