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- PDB-5c7i: Mouse sperm Glyceraldehyde-3-phosphate dehydrogenase: apo enzyme -

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Basic information

Entry
Database: PDB / ID: 5c7i
TitleMouse sperm Glyceraldehyde-3-phosphate dehydrogenase: apo enzyme
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, testis-specific
KeywordsOXIDOREDUCTASE / testis-specific metabolic
Function / homology
Function and homology information


Gluconeogenesis / sperm fibrous sheath / Glycolysis / sperm principal piece / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / positive regulation of glycolytic process / glycolytic process ...Gluconeogenesis / sperm fibrous sheath / Glycolysis / sperm principal piece / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / positive regulation of glycolytic process / glycolytic process / cilium / 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
Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.0098 Å
AuthorsDanshina, P. / Betts, L. / O'Brien, D.
CitationJournal: Mol. Hum. Reprod. / Year: 2016
Title: Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme.
Authors: Danshina, P.V. / Qu, W. / Temple, B.R. / Rojas, R.J. / Miley, M.J. / Machius, M. / Betts, L. / O'Brien, D.A.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific


Theoretical massNumber of molelcules
Total (without water)72,4182
Polymers72,4182
Non-polymers00
Water8,197455
1
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific

O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific


Theoretical massNumber of molelcules
Total (without water)144,8374
Polymers144,8374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area15460 Å2
ΔGint-78 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.717, 86.717, 158.358
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11R-601-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase, testis-specific / Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic ...Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic glyceraldehyde-3-phosphate dehydrogenase


Mass: 36209.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gapdhs, Gapd-s, Gapds / Production host: Escherichia coli (E. coli)
References: UniProt: Q64467, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1:1 mixture of protein at 3 mg/mL with 20% PEG3350, 0.1 M Bis-Tris-propane pH 6.5, 0.2 M potassium thiocyanate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.0098→30.6 Å / Num. obs: 44704 / % possible obs: 95.9 % / Redundancy: 3.5 % / Net I/σ(I): 23.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.0098→30.598 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1997 4.47 %Random
Rwork0.1784 42707 --
obs0.1797 44704 95.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.53 Å2 / Biso mean: 31.8463 Å2 / Biso min: 10.94 Å2
Refinement stepCycle: final / Resolution: 2.0098→30.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 0 455 5537
Biso mean---35.17 -
Num. residues----666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055192
X-RAY DIFFRACTIONf_angle_d0.9227058
X-RAY DIFFRACTIONf_chiral_restr0.059798
X-RAY DIFFRACTIONf_plane_restr0.004914
X-RAY DIFFRACTIONf_dihedral_angle_d13.0961890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0098-2.06010.25191340.21942918305293
2.0601-2.11580.2371350.20862921305694
2.1158-2.1780.23121410.19722955309694
2.178-2.24830.24241420.18952972311494
2.2483-2.32860.22291380.18462933307195
2.3286-2.42180.1951420.18693024316695
2.4218-2.5320.23231390.19272989312896
2.532-2.66540.23951420.1943052319496
2.6654-2.83230.24361410.19933057319896
2.8323-3.05080.24431440.18923078322297
3.0508-3.35750.17991460.18683111325797
3.3575-3.84250.2221440.16983131327598
3.8425-4.83810.15621530.14363206335998
4.8381-30.60120.18911560.16733360351699

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