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- PDB-9fl1: Apo Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 9fl1
TitleApo Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori
ComponentsGlyceraldehyde-3-phosphate dehydrogenase (Gap)
KeywordsOXIDOREDUCTASE / Apo enzyme NAD(P) Oxdative phosphorylation Nucleotide binding domain
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase (Gap)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsElliott, P.R. / Moody, P.C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: structure and coenzyme specificity of a Helicobacter pylori glyceraldehyde 3-phosphate dehydrogenase (GapA)
Authors: Foster, S. / Eliott, P.R. / Basran, J. / Moody, P.C.E.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)
B: Glyceraldehyde-3-phosphate dehydrogenase (Gap)
C: Glyceraldehyde-3-phosphate dehydrogenase (Gap)
D: Glyceraldehyde-3-phosphate dehydrogenase (Gap)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,52918
Polymers144,2774
Non-polymers1,25214
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-152 kcal/mol
Surface area45590 Å2
Unit cell
Length a, b, c (Å)75.160, 100.617, 97.792
Angle α, β, γ (deg.)90.000, 93.696, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase (Gap)


Mass: 36069.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Tetramer / Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1346 / Plasmid: pET151/DgapA / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta DE3 / References: UniProt: O25902
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 17% w/v PEG8000, 100mM Hepes, 12mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.74→95.4 Å / Num. obs: 147140 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 19
Reflection shellResolution: 1.74→1.82 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7357 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→95.346 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.154 / SU B: 5.833 / SU ML: 0.082 / Average fsc free: 0.9741 / Average fsc work: 0.9878 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1995 7374 5.012 %
Rwork0.1498 139766 -
all0.152 --
obs-147140 99.053 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.598 Å20 Å23.3 Å2
2---0.82 Å20 Å2
3----1.194 Å2
Refinement stepCycle: LAST / Resolution: 1.74→95.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9706 0 75 1006 10787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01210269
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610014
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.80213966
X-RAY DIFFRACTIONr_angle_other_deg0.571.75823092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07251334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.696558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.263101814
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.89210420
X-RAY DIFFRACTIONr_chiral_restr0.0810.21676
X-RAY DIFFRACTIONr_chiral_restr_other0.0070.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022227
X-RAY DIFFRACTIONr_nbd_refined0.2170.22037
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.29211
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24988
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.25349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2706
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_metal_ion_refined0.10.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.221
X-RAY DIFFRACTIONr_nbd_other0.1870.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.223
X-RAY DIFFRACTIONr_mcbond_it7.2732.665252
X-RAY DIFFRACTIONr_mcbond_other7.2712.665252
X-RAY DIFFRACTIONr_mcangle_it10.2514.786614
X-RAY DIFFRACTIONr_mcangle_other10.2514.786615
X-RAY DIFFRACTIONr_scbond_it8.8683.1255017
X-RAY DIFFRACTIONr_scbond_other8.863.1245015
X-RAY DIFFRACTIONr_scangle_it12.9555.5537352
X-RAY DIFFRACTIONr_scangle_other12.9545.5537353
X-RAY DIFFRACTIONr_lrange_it19.76628.25611389
X-RAY DIFFRACTIONr_lrange_other19.00227.95711222
X-RAY DIFFRACTIONr_rigid_bond_restr4.269320283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.74-1.7860.254930.20192450.204109260.9620.98189.12690.171
1.786-1.8340.2215130.18101400.182106660.9720.98399.87810.151
1.834-1.8880.2285300.16698300.169103700.9730.98699.90360.138
1.888-1.9460.1965030.1595650.152100780.9770.98899.90080.125
1.946-2.0090.2044740.14593000.14897840.9730.98999.89780.124
2.009-2.080.2064530.14790040.1594700.9720.9999.86270.129
2.08-2.1580.2014490.13886600.14191140.9730.9999.94510.124
2.158-2.2470.2014380.13683230.13987690.9750.9999.90880.124
2.247-2.3460.2054160.12980250.13384460.9760.99199.94080.121
2.346-2.4610.24150.13576410.13880680.9750.99199.85130.128
2.461-2.5940.2063990.13672740.1476820.9760.9999.88280.13
2.594-2.7510.2013890.13368450.13672370.9760.9999.95850.133
2.751-2.9410.1983500.14564700.14768270.9730.98899.89750.149
2.941-3.1760.2373130.16260480.16663650.9640.98599.93720.172
3.176-3.4790.2093100.16855580.17158730.9780.98699.91490.181
3.479-3.8890.2022810.1650040.16252910.9780.98799.88660.177
3.889-4.4890.1662290.12644780.12847090.9850.99199.95750.153
4.489-5.4950.1691900.14137670.14239600.9860.99199.92420.175
5.495-7.7590.1931450.17729650.17831110.9810.98699.96790.216
7.759-95.3460.16840.18316230.18217500.9850.98297.54290.256

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