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- PDB-4x5u: X-ray crystal structure of CagL at pH 4.2 -

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Basic information

Entry
Database: PDB / ID: 4x5u
TitleX-ray crystal structure of CagL at pH 4.2
ComponentsCag pathogenicity island protein (Cag18)
KeywordsCELL ADHESION / RGD Motif / Type IV Secretion System / Integrin
Function / homologyCag pathogenicity island protein (Cag18)
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSundberg, E.J. / Bonsor, D.A. / Diederichs, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Integrin Engagement by the Helical RGD Motif of the Helicobacter pylori CagL Protein Is Regulated by pH-induced Displacement of a Neighboring Helix.
Authors: Bonsor, D.A. / Pham, K.T. / Beadenkopf, R. / Diederichs, K. / Haas, R. / Beckett, D. / Fischer, W. / Sundberg, E.J.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cag pathogenicity island protein (Cag18)


Theoretical massNumber of molelcules
Total (without water)25,8781
Polymers25,8781
Non-polymers00
Water543
1
A: Cag pathogenicity island protein (Cag18)

A: Cag pathogenicity island protein (Cag18)


Theoretical massNumber of molelcules
Total (without water)51,7572
Polymers51,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7440 Å2
ΔGint-72 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.018, 63.018, 243.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

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Components

#1: Protein Cag pathogenicity island protein (Cag18)


Mass: 25878.434 Da / Num. of mol.: 1 / Fragment: RGD motif (UNP residues 21-237)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: C694_02780, HP_0539 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: O25272
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 30% v/v ethanol, 200 mM sodium phosphate/citric acid, pH 4.2, 5% w/v PEG 1000, 1% v/v glycerol, Microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→54.58 Å / Num. obs: 13696 / % possible obs: 100 % / Redundancy: 37.2 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 39.5 % / Rmerge(I) obs: 5.247 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0102refinement
Blu-Icedata collection
XDSdata scaling
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3zci

3zci


Resolution: 2.3→54.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 31.108 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31283 675 5 %RANDOM
Rwork0.25449 ---
obs0.25734 12955 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.162 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å21.4 Å20 Å2
2--2.79 Å20 Å2
3----9.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 3 1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191661
X-RAY DIFFRACTIONr_bond_other_d0.0020.021665
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9922228
X-RAY DIFFRACTIONr_angle_other_deg0.84633839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1315203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.68826.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29815347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.728157
X-RAY DIFFRACTIONr_chiral_restr0.0630.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
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_it1.3896.235818
X-RAY DIFFRACTIONr_mcbond_other1.3886.232817
X-RAY DIFFRACTIONr_mcangle_it2.3269.3421019
X-RAY DIFFRACTIONr_mcangle_other2.3259.3461020
X-RAY DIFFRACTIONr_scbond_it1.6886.49842
X-RAY DIFFRACTIONr_scbond_other1.6896.484840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8599.641208
X-RAY DIFFRACTIONr_long_range_B_refined4.03948.1691896
X-RAY DIFFRACTIONr_long_range_B_other4.03848.1921897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 44 -
Rwork0.459 932 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1839-2.6498-2.25894.65554.33767.6766-0.17440.3967-0.0899-0.4214-0.47080.5413-0.4083-1.21360.64520.35090.0042-0.11930.27110.00690.213823.857-5.03210.896
21.1649-0.1123-1.93351.49111.22279.4204-0.1361-0.0755-0.13180.173-0.13910.2070.5315-0.07180.27530.11380.00170.01460.04110.01080.135125.906-5.80134.429
30.64190.52311.92880.96563.061711.9850.06510.0699-0.07270.00070.05930.08060.29430.2749-0.12450.2294-0.0435-0.04720.06010.0090.106624.867-7.067-45.386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 59
2X-RAY DIFFRACTION2A60 - 184
3X-RAY DIFFRACTION3A185 - 239

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