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- PDB-6iqt: Crystal Structure of CagV, a VirB8 homolog of T4SS from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 6iqt
TitleCrystal Structure of CagV, a VirB8 homolog of T4SS from Helicobacter pylori Strain 26695
ComponentsCag pathogenicity island protein (Cag10)
KeywordsPROTEIN BINDING / Helicobacter pylori / Cag pathogenicity island / type IV secretion system / VirB8 / CagV / Crystal structure
Function / homologyBacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / membrane => GO:0016020 / Cag pathogenicity island protein (Cag10)
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.922 Å
AuthorsWu, X. / Zhao, Y. / Sun, L. / Jiang, M. / Wang, Q. / Wang, Q. / Yang, W. / Wu, Y.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structure of CagV, the Helicobacter pylori homologue of the T4SS protein VirB8.
Authors: Wu, X. / Zhao, Y. / Sun, L. / Jiang, M. / Wang, Q. / Wang, Q. / Yang, W. / Wu, Y.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 29, 2020Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cag pathogenicity island protein (Cag10)
B: Cag pathogenicity island protein (Cag10)
C: Cag pathogenicity island protein (Cag10)
D: Cag pathogenicity island protein (Cag10)


Theoretical massNumber of molelcules
Total (without water)77,4254
Polymers77,4254
Non-polymers00
Water5,747319
1
A: Cag pathogenicity island protein (Cag10)
B: Cag pathogenicity island protein (Cag10)


Theoretical massNumber of molelcules
Total (without water)38,7122
Polymers38,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cag pathogenicity island protein (Cag10)
D: Cag pathogenicity island protein (Cag10)


Theoretical massNumber of molelcules
Total (without water)38,7122
Polymers38,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.026, 96.851, 99.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cag pathogenicity island protein (Cag10)


Mass: 19356.164 Da / Num. of mol.: 4 / Fragment: UNP residues 74-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: HP_0530 / Plasmid: Pet32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25265
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.41 % / Description: diamon
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG2000MME(v/v), 0.3M trimethymaline n-oxidedehydrate, 0.1M Tris-HCl pH 8.5 buffer
PH range: 8.0-8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.922→50 Å / Num. obs: 49731 / % possible obs: 98.2 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Rrim(I) all: 0.167 / Χ2: 1.36 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.965.72.09216290.3010.852.2741.10165.1
1.96-29.71.57224830.7590.521.6581.121100
2-2.04121.324860.8510.3921.3581.222100
2.04-2.0813.31.18225230.8820.3391.231.234100
2.17-2.23140.65724960.9540.1840.6831.384100
2.23-2.2913.90.54925170.9620.1540.5711.425100
2.29-2.36140.47524910.970.1330.4931.431100
2.36-2.43140.40425470.9750.1130.421.43100
2.43-2.5214.10.33624940.980.0940.3491.43100
2.52-2.62140.27925180.9860.0780.2891.463100
2.62-2.74140.23125100.9880.0640.241.44100
2.74-2.88140.225220.9890.0560.2081.448100
2.88-3.06140.17125290.9880.0480.1771.456100
3.06-3.313.90.14925570.9910.0420.1551.482100
3.3-3.6313.80.13925490.990.0390.1451.55100
3.63-4.1613.60.13425750.9920.0370.1391.543100
4.16-5.24130.1126050.9940.0320.1151.185100
5.24-5012.20.09227280.9940.0280.0960.86999.3
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.922→49.574 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2108 2346 4.8 %
Rwork0.1841 --
obs0.1854 48899 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.41 Å2 / Biso mean: 37.3744 Å2 / Biso min: 16.43 Å2
Refinement stepCycle: final / Resolution: 1.922→49.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 0 319 4669
Biso mean---43.38 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074422
X-RAY DIFFRACTIONf_angle_d0.865953
X-RAY DIFFRACTIONf_chiral_restr0.058682
X-RAY DIFFRACTIONf_plane_restr0.005753
X-RAY DIFFRACTIONf_dihedral_angle_d3.1432703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9221-1.96140.3453900.25211886197669
1.9614-2.0040.25321240.225927472871100
2.004-2.05060.2821270.214227892916100
2.0506-2.10190.25141230.207127792902100
2.1019-2.15870.24731430.198127482891100
2.1587-2.22230.23381370.193127412878100
2.2223-2.2940.241620.188327322894100
2.294-2.3760.25811530.190827602913100
2.376-2.47110.23121630.18727582921100
2.4711-2.58360.19991320.191627752907100
2.5836-2.71980.23041570.190327732930100
2.7198-2.89020.21141270.19327882915100
2.8902-3.11330.23061330.191528232956100
3.1133-3.42650.2281290.181628072936100
3.4265-3.92220.17381620.167328122974100
3.9222-4.94080.16881270.156528773004100
4.9408-49.59050.20411570.1932958311599
Refinement TLS params.Method: refined / Origin x: 30.1712 Å / Origin y: 7.7428 Å / Origin z: -11.97 Å
111213212223313233
T0.1811 Å2-0.0183 Å20.0144 Å2-0.1947 Å2-0.01 Å2--0.2156 Å2
L0.2885 °2-0.1068 °2-0.2657 °2-0.2807 °20.1816 °2--0.6851 °2
S-0.0315 Å °0.0084 Å °-0.0312 Å °-0.0084 Å °0.0178 Å °0.041 Å °0.0226 Å °-0.0291 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA86 - 228
2X-RAY DIFFRACTION1allB92 - 228
3X-RAY DIFFRACTION1allC91 - 228
4X-RAY DIFFRACTION1allD88 - 228
5X-RAY DIFFRACTION1allS1 - 319

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