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

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Basic information

Entry
Database: PDB / ID: 3qrc
TitleThe crystal structure of Ail, the attachment invasion locus protein of Yersinia pestis, in complex with the heparin analogue sucrose octasulfate
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. / Enterobacterial virulence outer membrane protein signature 2. / Virulence-related outer membrane protein / 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
sucrose octasulfate / Attachment invasion locus protein / Outer membrane protein X
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment invasion locus protein
B: Attachment invasion locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,35811
Polymers35,2472
Non-polymers4,1119
Water2,180121
1
A: Attachment invasion locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2194
Polymers17,6241
Non-polymers1,5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Attachment invasion locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1397
Polymers17,6241
Non-polymers2,5156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.382, 91.382, 47.496
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 26:84 or resseq 89:182 )
211chain B and (resseq 26:84 or resseq 89:182 )

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Components

#1: Protein Attachment invasion locus protein / Ail


Mass: 17623.596 Da / Num. of mol.: 2 / 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: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 30% PEG400, 0.2 M lithium sulfate, 0.1 M citric acid, pH 3.0, 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: Jan 4, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→79.057 Å / Num. all: 37771 / Num. obs: 37771 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rsym value: 0.103 / Net I/σ(I): 15.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.11 / Rsym value: 0.713 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QRA

3qra


Resolution: 1.852→32.928 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 21.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2213 1887 5 %
Rwork0.2036 --
obs0.2045 37761 99.96 %
all-37771 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.539 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4567 Å2-0 Å20 Å2
2---0.4567 Å20 Å2
3---0.9133 Å2
Refinement stepCycle: LAST / Resolution: 1.852→32.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 202 121 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152829
X-RAY DIFFRACTIONf_angle_d1.3813551
X-RAY DIFFRACTIONf_dihedral_angle_d24.433989
X-RAY DIFFRACTIONf_chiral_restr0.092363
X-RAY DIFFRACTIONf_plane_restr0.004425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1156X-RAY DIFFRACTIONPOSITIONAL
12B1156X-RAY DIFFRACTIONPOSITIONAL0.076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8516-1.91780.27561930.29163583X-RAY DIFFRACTION100
1.9178-1.99460.2662000.22373577X-RAY DIFFRACTION100
1.9946-2.08530.22771970.19433588X-RAY DIFFRACTION100
2.0853-2.19530.20591870.1823617X-RAY DIFFRACTION100
2.1953-2.33280.22731750.18253570X-RAY DIFFRACTION100
2.3328-2.51280.21241720.19723613X-RAY DIFFRACTION100
2.5128-2.76560.23911860.19443598X-RAY DIFFRACTION100
2.7656-3.16550.21161880.19043579X-RAY DIFFRACTION100
3.1655-3.98710.20481940.1913591X-RAY DIFFRACTION100
3.9871-32.93320.2231950.22063558X-RAY DIFFRACTION100
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)
12.33510.781-1.2021.6937-1.74312.5282-0.12950.13670.1045-0.35870.0714-0.02240.5121-0.25480.04960.2212-0.0590.01220.15450.00660.104727.5087-5.93116.2962
22.49180.78211.17791.61381.75542.4983-0.11550.15-0.1259-0.32770.0750.0292-0.50910.26810.03970.2124-0.0606-0.0130.1464-0.00480.092718.1063-20.5189-17.5598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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