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- PDB-3zci: Crystal structure of Helicobacter pylori T4SS protein CagL in a c... -

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Basic information

Entry
Database: PDB / ID: 3zci
TitleCrystal structure of Helicobacter pylori T4SS protein CagL in a cubic crystal form with a distorted helical conformation of the RGD-motif
ComponentsCAG PATHOGENICITY ISLAND PROTEIN (CAG18)
KeywordsPROTEIN BINDING / KKQEK / SER MUTANT / ADHESION / RGD MOTIF / INTEGRIN BINDING / TYPE IV SECRETION / T4S / VIRULENCE / CAG18 / HP0539
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1660 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Meso-2,3-Butanediol / 1,4-DIETHYLENE DIOXIDE / Cag pathogenicity island protein (Cag18)
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.201 Å
AuthorsBarden, S. / Niemann, H.H.
CitationJournal: Structure / Year: 2013
Title: A Helical Rgd Motif Promoting Cell Adhesion: Crystal Structures of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl
Authors: Barden, S. / Lange, S. / Tegtmeyer, N. / Conradi, J. / Sewald, N. / Backert, S. / Niemann, H.H.
History
DepositionNov 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAG PATHOGENICITY ISLAND PROTEIN (CAG18)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,79911
Polymers24,9411
Non-polymers85810
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.002, 181.002, 181.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CAG PATHOGENICITY ISLAND PROTEIN (CAG18) / CAGL


Mass: 24940.545 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-237 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: O25272

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Non-polymers , 5 types, 123 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-BU9 / Meso-2,3-Butanediol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMESO-2,3-BUTANEDIOL (BU9): CRYO PROTECTANT 1,4-DIETHYLENE DIOXIDE (DIO): CRYSTALLIZATION COCKTAIL ...MESO-2,3-BUTANEDIOL (BU9): CRYO PROTECTANT 1,4-DIETHYLENE DIOXIDE (DIO): CRYSTALLIZATION COCKTAIL COMPOUND SULFATE ION (SO4): CRYSTALLIZATION COCKTAIL COMPOUND CHLORIDE ION (CL): CRYSTALLIZATION COCKTAIL COMPOUND SELENOMETHIONINE (MSE): CO-TRANSLATIONALLY INCORPORATED FOR PHASING
Sequence detailsSURFACE ENTROPY REDUCTION MUTANT KKQEK

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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: 5 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: PROTEIN CONCENTRATION:7 MG/ML. RESERVOIR: 100 MM MES PH6.5, 1.2 M AMMONIUM SULPHATE, 2-4 % 1,4 DIOXANE. VAPOR DIFFUSION AT 277 K WITH DROP RATIO OF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97814, 0.97814, 0.97847
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978141
20.978471
ReflectionResolution: 2.2→20 Å / Num. obs: 24942 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 37.06 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.201→19.868 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 23.4 / Stereochemistry target values: ML / Details: SECONDARY STRUCTURE RESTRAINTS APPLIED
RfactorNum. reflection% reflection
Rfree0.2446 1286 5.2 %
Rwork0.2075 --
obs0.2094 24907 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.58 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 46.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.8678 Å20 Å20 Å2
2--1.8678 Å20 Å2
3---1.8678 Å2
Refinement stepCycle: LAST / Resolution: 2.201→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 52 113 1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121886
X-RAY DIFFRACTIONf_angle_d1.2922543
X-RAY DIFFRACTIONf_dihedral_angle_d16.831747
X-RAY DIFFRACTIONf_chiral_restr0.075292
X-RAY DIFFRACTIONf_plane_restr0.008324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2015-2.28950.27341480.29162614X-RAY DIFFRACTION100
2.2895-2.39350.29991440.25972573X-RAY DIFFRACTION100
2.3935-2.51950.31221490.26032616X-RAY DIFFRACTION100
2.5195-2.6770.28911430.2322591X-RAY DIFFRACTION100
2.677-2.88310.28481530.21712614X-RAY DIFFRACTION100
2.8831-3.17220.25981370.20432619X-RAY DIFFRACTION100
3.1722-3.62880.20411420.18132631X-RAY DIFFRACTION100
3.6288-4.56270.21971350.17112649X-RAY DIFFRACTION100
4.5627-19.86830.22471350.21342714X-RAY DIFFRACTION100

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