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- PDB-3cmc: Thioacylenzyme intermediate of Bacillus stearothermophilus phosph... -

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Basic information

Entry
Database: PDB / ID: 3cmc
TitleThioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / microspectrophotometry / reaction intermediate / dehydrogenase / phosphate binding site / thioacylenzyme / Glycolysis / NAD
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 / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsMoniot, S. / Vonrhein, C. / Bricogne, G. / Didierjean, C. / Corbier, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Trapping of the Thioacylglyceraldehyde-3-phosphate Dehydrogenase Intermediate from Bacillus stearothermophilus: DIRECT EVIDENCE FOR A FLIP-FLOP MECHANISM
Authors: Moniot, S. / Bruno, S. / Vonrhein, C. / Didierjean, C. / Boschi-Muller, S. / Vas, M. / Bricogne, G. / Branlant, G. / Mozzarelli, A. / Corbier, C.
History
DepositionMar 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)149,82639
Polymers143,9644
Non-polymers5,86235
Water31,3461740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27300 Å2
ΔGint-433.4 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.670, 122.630, 81.790
Angle α, β, γ (deg.)90.000, 111.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules OPQR

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


Mass: 35991.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: gap / Plasmid: pBluescript II SK / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 6 types, 1775 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1740 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.7 M Ammonium Sulfate, 100 mM Tris-HCl buffer pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.806 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2006
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.806 Å / Relative weight: 1
ReflectionResolution: 1.77→29.5 Å / Num. all: 142733 / Num. obs: 142733 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 32.1
Reflection shellResolution: 1.77→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.5 / Num. unique all: 20259 / % possible all: 92.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
BUSTER-TNT2.3.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→29.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 7133 5 %RANDOM
Rwork0.161 ---
all0.163 149866 --
obs0.163 142733 97.68 %-
Displacement parametersBiso mean: 25.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-2.185 Å2
2---1.163 Å20 Å2
3---0.863 Å2
Refine analyzeLuzzati coordinate error obs: 0.184 Å
Refinement stepCycle: LAST / Resolution: 1.77→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 358 1740 12198
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011110182
X-RAY DIFFRACTIONt_angle_deg1.266149772
X-RAY DIFFRACTIONt_dihedral_angle_d16.96422670
X-RAY DIFFRACTIONIMPROPER ANGLES (DEGREES)25.962120
X-RAY DIFFRACTIONt_trig_c_planes0.0112792
X-RAY DIFFRACTIONt_gen_planes0.0216085
X-RAY DIFFRACTIONt_it1.6861101820
X-RAY DIFFRACTIONt_nbd0.0562245
LS refinement shellResolution: 1.77→1.88 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.24 1011 4.99 %
Rwork0.193 19248 -
all0.195 20259 -
obs--97.68 %

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