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- PDB-1g6o: CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ATPASE, HP0525, IN C... -

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Basic information

Entry
Database: PDB / ID: 1g6o
TitleCRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH ADP
ComponentsCAG-ALPHA
KeywordsHYDROLASE / ATPase / type IV secretion system / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


secretion by the type IV secretion system / type IV secretion system complex / nucleotide binding / ATP hydrolysis activity / metal ion binding / identical protein binding
Similarity search - Function
Type IV secretion system protein VirB11 / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich ...Type IV secretion system protein VirB11 / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / : / Cag alpha
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsYeo, H.J. / Savvides, S.N. / Herr, A.B. / Lanka, E. / Waksman, G. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Mol.Cell / Year: 2000
Title: Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV secretion system.
Authors: Yeo, H.J. / Savvides, S.N. / Herr, A.B. / Lanka, E. / Waksman, G.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 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 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
A: CAG-ALPHA
B: CAG-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2139
Polymers75,8282
Non-polymers1,3857
Water5,314295
1
A: CAG-ALPHA
B: CAG-ALPHA
hetero molecules

A: CAG-ALPHA
B: CAG-ALPHA
hetero molecules

A: CAG-ALPHA
B: CAG-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,64027
Polymers227,4856
Non-polymers4,15521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area29790 Å2
ΔGint-89 kcal/mol
Surface area80110 Å2
MethodPISA, PQS
2
A: CAG-ALPHA
B: CAG-ALPHA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)463,28154
Polymers454,97112
Non-polymers8,31042
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area62650 Å2
ΔGint-207 kcal/mol
Surface area157160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.620, 112.620, 234.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe functional hexamer can be generated from the two molecules in the asymmetric unit by three fold axes intrinsic to space group P6(3)22

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Components

#1: Protein CAG-ALPHA / TRAFFIC ATPASE


Mass: 37914.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: PWP4760 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: GenBank: 8843975, UniProt: Q7BK04*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1000, calcium acetate, glycerol, ADP-Mg, Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
319-21 %PEG10001reservoir
40.2 Mcalcium acetate1reservoir
515 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→500 Å / Num. all: 137723 / Num. obs: 27352 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.158 / % possible all: 71.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 137723
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 71.4 % / Mean I/σ(I) obs: 5.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 583702.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1354 5 %RANDOM
Rwork0.224 ---
obs0.224 27326 88.8 %-
all-137723 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 32 Å2 /
Baniso -2Baniso -3
2-0 Å20 Å2
3--0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 82 295 5482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.962.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 111 4.8 %
Rwork0.293 2203 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP.PARAMADP.TOPO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION49PEG.PARAM9PEG.TOPO
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scangle_it3.962.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.293

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