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- PDB-5h3v: Crystal structure of a Type IV Secretion System Component CagX in... -

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Basic information

Entry
Database: PDB / ID: 5h3v
TitleCrystal structure of a Type IV Secretion System Component CagX in Helicobacter pylori
ComponentsCag8
KeywordsPROTEIN BINDING / Helicobacter pylori / cytotoxin-associated gene pathogenicity island (cagPAI) / Type IV secretion system / CagX
Function / homologyType IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / Cag pathogenicity island protein (Cag8) / Cag8
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, J. / Wu, Y. / Zhao, Y. / Sun, L. / Keegan, R.M. / Liu, Y. / Isupov, M.N.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the type IV secretion system component CagX from Helicobacter pylori
Authors: Zhang, J. / Fan, F. / Zhao, Y. / Sun, L. / Liu, Y. / Keegan, R.M. / Isupov, M.N. / Wu, Y.
History
DepositionOct 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_reflns_twin
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_reflns_twin.operator

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cag8
B: Cag8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8335
Polymers23,6072
Non-polymers2263
Water2,342130
1
A: Cag8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9243
Polymers11,8041
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cag8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9102
Polymers11,8041
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.080, 61.620, 48.420
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cag8 / cag pathogenicity island protein cag8


Mass: 11803.538 Da / Num. of mol.: 2 / Fragment: UNP residues 396-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: cag8, wsv002 / Plasmid: pET-32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6VRS3, UniProt: O25263*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 27% PEG4K, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.509
11-h,-k,l20.491
ReflectionResolution: 1.4→38.07 Å / Num. obs: 34978 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / CC1/2: 0.997 / Rsym value: 0.05 / Net I/σ(I): 12.3
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1587 / CC1/2: 0.803 / Rsym value: 0.347 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
MOLREPMORDAphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jqo

3jqo


Resolution: 1.4→38.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24887 1699 4.9 %RANDOM
Rwork0.20025 ---
obs0.20255 33259 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.553 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å2-0.32 Å2
2--14.02 Å20 Å2
3----10.82 Å2
Refinement stepCycle: 1 / Resolution: 1.4→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 15 130 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9822603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33724.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08115348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9621510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6761.4876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4252.0911105
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8821.5241017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.35125.8417606
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.396→1.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 45 -
Rwork0.291 1283 -
obs--46.73 %

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