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- PDB-2g3v: Crystal structure of CagS (HP0534, Cag13) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2g3v
TitleCrystal structure of CagS (HP0534, Cag13) from Helicobacter pylori
Components
  • (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)
  • CAG pathogenicity island protein 13
KeywordsUNKNOWN FUNCTION / Helicobacter pylori / pathogenicity island / Type IV secretion system
Function / homologyCAG pathogenicity island protein 13, CagS / CAG pathogenicity island protein 13 / CagS superfamily / Cag pathogenicity island protein S of Helicobacter pylori / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / CAG pathogenicity island protein 13
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCendron, L. / Tasca, E. / Angelini, A. / Seydel, A. / Battistutta, R. / Montecucco, C. / Zanotti, G.
Citation
Journal: To be Published
Title: Crystal structure of CagS from helicobacter pylori
Authors: Cendron, L. / Tasca, E. / Angelini, A. / Seydel, A. / Battistutta, R. / Montecucco, C. / Zanotti, G.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of CagZ, a protein from the Helicobacter pylori pathogenicity island that encodes for a type IV secretion system
Authors: Cendron, L. / Seydel, A. / Angelini, A. / Battistutta, R. / Zanotti, G.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAG pathogenicity island protein 13
B: CAG pathogenicity island protein 13
C: CAG pathogenicity island protein 13
D: CAG pathogenicity island protein 13
E: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)
F: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)
G: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)
H: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Theoretical massNumber of molelcules
Total (without water)104,9748
Polymers104,9748
Non-polymers00
Water4,288238
1
A: CAG pathogenicity island protein 13
E: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Theoretical massNumber of molelcules
Total (without water)26,2442
Polymers26,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-7 kcal/mol
Surface area9840 Å2
MethodPISA
2
B: CAG pathogenicity island protein 13
F: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Theoretical massNumber of molelcules
Total (without water)26,2442
Polymers26,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-7 kcal/mol
Surface area10080 Å2
MethodPISA
3
C: CAG pathogenicity island protein 13
G: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Theoretical massNumber of molelcules
Total (without water)26,2442
Polymers26,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-7 kcal/mol
Surface area9900 Å2
MethodPISA
4
D: CAG pathogenicity island protein 13
H: (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Theoretical massNumber of molelcules
Total (without water)26,2442
Polymers26,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-7 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.360, 124.360, 55.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
CAG pathogenicity island protein 13


Mass: 25536.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: cagS, cag13, HP0534 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97227
#2: Protein/peptide
(UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)


Mass: 706.735 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M KBr, 25% PEG 2000 MME, 0.1M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792, 0.9794, 0.9756, 1.0
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2005 / Details: Mirrors
RadiationMonochromator: Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97561
411
ReflectionResolution: 2.3→51 Å / Num. all: 38297 / Num. obs: 38297 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 6.7 Å2 / Rsym value: 0.011 / Net I/σ(I): 5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5569 / Rsym value: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2250186.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3691 9.6 %RANDOM
Rwork0.219 ---
obs0.219 38258 99.8 %-
all-38297 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1075 Å2 / ksol: 0.40001 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2--3.39 Å20 Å2
3----6.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 0 238 5790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 446 9.8 %
Rwork0.238 5720 -
obs-4287 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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