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- PDB-3syj: Crystal structure of the Haemophilus influenzae Hap adhesin -

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Basic information

Entry
Database: PDB / ID: 3syj
TitleCrystal structure of the Haemophilus influenzae Hap adhesin
ComponentsAdhesion and penetration protein autotransporter
KeywordsCELL ADHESION / Bacterial aggregation and biofilm formation / self-associating autotransporter (SAAT) / oligomerization / beta helix fold / membrane
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / membrane => GO:0016020 / periplasmic space / cell adhesion / serine-type endopeptidase activity / cell surface / extracellular region / identical protein binding
Similarity search - Function
Pertactin, central region / Pertactin / Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. ...Pertactin, central region / Pertactin / Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Thrombin, subunit H - #120 / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Serine proteases, trypsin family, serine active site / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adhesion and penetration protein autotransporter
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMeng, G.
CitationJournal: Embo J. / Year: 2011
Title: Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation
Authors: Meng, G. / Spahich, N. / Kenjale, R. / Waksman, G. / St Geme III, J.W.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Adhesion and penetration protein autotransporter


Theoretical massNumber of molelcules
Total (without water)112,1391
Polymers112,1391
Non-polymers00
Water14,106783
1
A: Adhesion and penetration protein autotransporter

A: Adhesion and penetration protein autotransporter


Theoretical massNumber of molelcules
Total (without water)224,2772
Polymers224,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465x-1/2,-y+3/2,-z1
Unit cell
Length a, b, c (Å)41.410, 137.200, 209.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe second HapS of the biological assembly mediated by the C-terminal SAAT domain is generated alone the p21 a-axis. The crystal packing reveals a remarkable oligomerization of (HapS-HapS)n related by a crystallographic two-fold screw axis (i.e. p21 a-axis), perpendicular to the axis of the helix.

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Components

#1: Protein Adhesion and penetration protein autotransporter / Hap adhesin / Adhesion and penetration protein / Adhesion and penetration protein translocator


Mass: 112138.531 Da / Num. of mol.: 1 / Fragment: Hap passenger domain (HapS), UNP residues 26-1036
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: DB117 / Gene: hap / Plasmid: pJS106 / Production host: Escherichia coli (E. coli)
References: UniProt: P45387, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate, 14% (w/v) PEG 4000, 100mM ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→68.6 Å / Num. obs: 60596 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 31.8 Å2 / Rsym value: 0.135 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rsym value: 0.588 / % possible all: 89

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3H09 and 2WXR

3h09

2wxr


Resolution: 2.2→68.6 Å / SU ML: 0.31 / σ(F): 0.01 / Phase error: 22.55 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 5174 5.1 %RANDOM
Rwork0.1865 ---
obs0.1885 60596 86.68 %-
all-60596 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.408 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8455 Å2-0 Å20 Å2
2---5.9874 Å2-0 Å2
3---4.1419 Å2
Refinement stepCycle: LAST / Resolution: 2.2→68.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 0 783 7968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057337
X-RAY DIFFRACTIONf_angle_d0.9189928
X-RAY DIFFRACTIONf_dihedral_angle_d17.6872640
X-RAY DIFFRACTIONf_chiral_restr0.061073
X-RAY DIFFRACTIONf_plane_restr0.0031320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.31351120.31311983X-RAY DIFFRACTION54
2.225-2.25120.34641150.33192154X-RAY DIFFRACTION59
2.2512-2.27860.39631590.32522272X-RAY DIFFRACTION61
2.2786-2.30750.3281580.29352446X-RAY DIFFRACTION66
2.3075-2.33790.32241220.27872537X-RAY DIFFRACTION69
2.3379-2.36990.30941240.28372677X-RAY DIFFRACTION73
2.3699-2.40370.29691390.26532930X-RAY DIFFRACTION78
2.4037-2.43960.321710.26653066X-RAY DIFFRACTION81
2.4396-2.47780.28391750.25273052X-RAY DIFFRACTION84
2.4778-2.51840.31511560.23633249X-RAY DIFFRACTION88
2.5184-2.56180.2861520.22843356X-RAY DIFFRACTION89
2.5618-2.60840.2561760.23353328X-RAY DIFFRACTION90
2.6084-2.65860.29241620.21613290X-RAY DIFFRACTION90
2.6586-2.71280.29151660.20643438X-RAY DIFFRACTION92
2.7128-2.77180.26261870.20223419X-RAY DIFFRACTION92
2.7718-2.83630.22171850.20263410X-RAY DIFFRACTION93
2.8363-2.90720.22482140.19963464X-RAY DIFFRACTION94
2.9072-2.98580.22471870.19153534X-RAY DIFFRACTION94
2.9858-3.07370.24132090.19183402X-RAY DIFFRACTION94
3.0737-3.17290.22822030.17733615X-RAY DIFFRACTION95
3.1729-3.28630.23471510.17143521X-RAY DIFFRACTION96
3.2863-3.41790.21731890.15153633X-RAY DIFFRACTION96
3.4179-3.57340.17392320.13563507X-RAY DIFFRACTION97
3.5734-3.76180.15772210.13463597X-RAY DIFFRACTION97
3.7618-3.99750.17691880.13063553X-RAY DIFFRACTION97
3.9975-4.30610.15891970.1243564X-RAY DIFFRACTION97
4.3061-4.73930.15151890.11893590X-RAY DIFFRACTION97
4.7393-5.42490.17371840.133558X-RAY DIFFRACTION97
5.4249-6.83380.17041780.16213600X-RAY DIFFRACTION95
6.8338-68.63330.21161730.18153551X-RAY DIFFRACTION96

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