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- PDB-9fob: Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter... -

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Basic information

Entry
Database: PDB / ID: 9fob
TitleGlyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori in Complex with NAPD (Holo)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase (Gap)
KeywordsOXIDOREDUCTASE / Holoenzyme 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
METHANOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyceraldehyde-3-phosphate dehydrogenase (Gap)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 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)153,42110
Polymers150,3834
Non-polymers3,0386
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: uncleaved his-tag and linker desnsity seen in A and B chains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-103 kcal/mol
Surface area45800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.938, 116.938, 95.474
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 37595.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: electron density for V5 epitope of linker for hexa-his tag visible in Chains A + B
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1346 / Plasmid: pET151/D / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3 / References: UniProt: O25902
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 100mM Tris, 36% v/v methanol, 1mM NADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→69.5 Å / Num. obs: 43460 / % possible obs: 96.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 5857 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.774 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.106 / SU ML: 0.231 / Cross valid method: FREE R-VALUE / ESU R Free: 0.329
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2414 2077 4.782 %
Rwork0.1746 41361 -
all0.178 --
obs-43438 96.826 %
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: 55.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.809 Å20.404 Å20 Å2
2--0.809 Å20 Å2
3----2.624 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10357 0 196 88 10641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210913
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610537
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.80414881
X-RAY DIFFRACTIONr_angle_other_deg0.4921.75824292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16651399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.769556
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.44458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.487101913
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.80510451
X-RAY DIFFRACTIONr_chiral_restr0.0660.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022349
X-RAY DIFFRACTIONr_nbd_refined0.220.22047
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.29681
X-RAY DIFFRACTIONr_nbtor_refined0.170.25187
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2322
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.224
X-RAY DIFFRACTIONr_nbd_other0.1640.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.212
X-RAY DIFFRACTIONr_mcbond_it4.2365.4465457
X-RAY DIFFRACTIONr_mcbond_other4.2335.4475457
X-RAY DIFFRACTIONr_mcangle_it5.9789.7836832
X-RAY DIFFRACTIONr_mcangle_other5.9789.7836833
X-RAY DIFFRACTIONr_scbond_it4.495.7555456
X-RAY DIFFRACTIONr_scbond_other4.4855.7555454
X-RAY DIFFRACTIONr_scangle_it6.60310.4438026
X-RAY DIFFRACTIONr_scangle_other6.60310.4428027
X-RAY DIFFRACTIONr_lrange_it8.25651.78611524
X-RAY DIFFRACTIONr_lrange_other8.25751.70911518
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
2.6-2.6670.3731200.22924200.23532930.9220.96977.13330.203
2.667-2.740.2571450.2326740.23132170.9560.97187.62820.203
2.74-2.8190.2941820.21628240.22131140.9510.97696.53180.189
2.819-2.9060.3011860.23928780.24330640.950.971000.212
2.906-30.271340.21628360.21829700.9550.9751000.191
3-3.1050.3481320.20927180.21428500.940.9711000.192
3.105-3.2220.2981420.20426300.20827720.9440.9751000.192
3.222-3.3530.2821060.19825440.20126500.9480.9781000.19
3.353-3.5010.258880.20624410.20825290.9570.9771000.202
3.501-3.6710.2751140.18723630.19124770.9560.9811000.187
3.671-3.8680.215980.17522070.17723050.9760.9831000.179
3.868-4.1010.2371080.1620500.16421580.970.9861000.171
4.101-4.3810.242840.15119880.15520720.9660.9871000.17
4.381-4.7280.1681020.1318140.13219160.9840.9911000.15
4.728-5.1740.183620.13417150.13517770.9780.991000.152
5.174-5.7750.155780.14315290.14416080.9860.98999.93780.158
5.775-6.650.268740.15713290.16214030.9680.9881000.169
6.65-8.10.172540.13611450.13812010.9830.98999.83350.152
8.1-11.2720.193420.1368250.1389290.9810.9993.32620.157
11.272-44.7740.298260.2524310.2555500.9420.96683.09090.28

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