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- PDB-3qra: The crystal structure of Ail, the attachment invasion locus prote... -

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Basic information

Entry
Database: PDB / ID: 3qra
TitleThe crystal structure of Ail, the attachment invasion locus protein of Yersinia pestis
ComponentsAttachment invasion locus protein
KeywordsCELL INVASION / beta-barrel protein / attachment and invasion virulence / laminin / heparin
Function / homology
Function and homology information


host outer membrane / cell outer membrane
Similarity search - Function
: / Enterobacterial virulence outer membrane protein signature 1. / Virulence-related outer membrane protein / Enterobacterial virulence outer membrane protein signature 2. / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Attachment invasion locus protein / Outer membrane protein X
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsYamashita, S. / Lukacik, P. / Noinaj, N. / Buchanan, S.K.
CitationJournal: Structure / Year: 2011
Title: Structural Insights into Ail-Mediated Adhesion in Yersinia pestis.
Authors: Yamashita, S. / Lukacik, P. / Barnard, T.J. / Noinaj, N. / Felek, S. / Tsang, T.M. / Krukonis, E.S. / Hinnebusch, B.J. / Buchanan, S.K.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment invasion locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7698
Polymers17,6241
Non-polymers2,1457
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.236, 50.236, 170.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Attachment invasion locus protein / Ail


Mass: 17623.596 Da / Num. of mol.: 1 / Fragment: UNP residues 27-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ail, YPO2905 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WCZ9, UniProt: Q8D0Z7*PLUS
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 34% PEG1000, 0.2 M potassium fluoride, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.7 Å / Num. all: 19652 / Num. obs: 19652 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.3 % / Rsym value: 0.058 / Net I/σ(I): 44.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.346 / % possible all: 68

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: dev_572)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJ8

1qj8


Resolution: 1.801→34.777 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 993 5.03 %RANDOM
Rwork0.1985 ---
obs0.1999 19652 93.1 %-
all-19652 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.233 Å2-0 Å20 Å2
2---7.233 Å20 Å2
3---9.9454 Å2
Refinement stepCycle: LAST / Resolution: 1.801→34.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 69 70 1316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141268
X-RAY DIFFRACTIONf_angle_d1.2591677
X-RAY DIFFRACTIONf_dihedral_angle_d14.762471
X-RAY DIFFRACTIONf_chiral_restr0.096162
X-RAY DIFFRACTIONf_plane_restr0.005209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.89560.27381080.23771978X-RAY DIFFRACTION71
1.8956-2.01430.23561220.17892375X-RAY DIFFRACTION84
2.0143-2.16980.17961620.16062678X-RAY DIFFRACTION96
2.1698-2.38810.1991570.17232831X-RAY DIFFRACTION100
2.3881-2.73360.21831520.18552866X-RAY DIFFRACTION100
2.7336-3.44360.21081490.17342892X-RAY DIFFRACTION100
3.4436-34.7830.25571430.22943120X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.6544 Å / Origin y: 19.8181 Å / Origin z: 24.9946 Å
111213212223313233
T0.1604 Å2-0.0015 Å2-0.0025 Å2-0.1382 Å20.0108 Å2--0.1509 Å2
L2.0061 °20.4707 °2-0.2839 °2-0.6626 °2-0.1065 °2--1.8223 °2
S0.098 Å °-0.0136 Å °0.0364 Å °-0.024 Å °-0.0897 Å °-0.2167 Å °-0.2047 Å °0.1129 Å °0.0225 Å °
Refinement TLS groupSelection details: chain A

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