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- PDB-5v8x: Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-... -

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Basic information

Entry
Database: PDB / ID: 5v8x
TitleMutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / GAPDH / GLYCOLYSIS
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / metal ion binding / identical protein binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSchormann, N. / Ulett, G.C. / Chattopadhyay, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Res CouncilFT110101048 Australia
CitationJournal: To Be Published
Title: Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)
Authors: Schormann, N. / Ulett, G.C. / Chattopadhyay, D.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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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)155,63012
Polymers152,8794
Non-polymers2,7518
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20170 Å2
ΔGint-139 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.104, 107.805, 91.432
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38219.867 Da / Num. of mol.: 4 / Mutation: Y288H, G289S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: gap, AX245_09885, DX05_09270, EN72_09590, RDF_1710, TH70_1537
Plasmid: pET15b / Cell line (production host): Rosetta(DE3)pLysS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ALW2, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20-27% PEG 4000, 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→107.8 Å / Num. obs: 26679 / % possible obs: 99.3 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.063 / Rrim(I) all: 0.141 / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.56 / CC1/2: 0.527 / Rpim(I) all: 0.764 / Rrim(I) all: 1.742 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SCALA0.5.17data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSOct. 2015data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JY6

5jy6


Resolution: 2.95→46.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 30.256 / SU ML: 0.512 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.513
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1298 4.9 %RANDOM
Rwork0.2218 ---
obs0.2242 25354 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.26 Å2 / Biso mean: 82.065 Å2 / Biso min: 33.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.03 Å2
2--0.03 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.95→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9904 0 180 20 10104
Biso mean--71.96 57.76 -
Num. residues----1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910238
X-RAY DIFFRACTIONr_bond_other_d0.0030.029407
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.94313917
X-RAY DIFFRACTIONr_angle_other_deg0.9882.98921825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60551305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95925.302447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.243151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1891552
X-RAY DIFFRACTIONr_chiral_restr0.0730.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021925
LS refinement shellResolution: 2.95→3.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 97 -
Rwork0.367 1851 -
all-1948 -
obs--99.85 %

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