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- PDB-2xi9: Pilus-presented adhesin, Spy0125 (Cpa), P1 form -

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Basic information

Entry
Database: PDB / ID: 2xi9
TitlePilus-presented adhesin, Spy0125 (Cpa), P1 form
ComponentsANCILLARY PROTEIN 1
KeywordsCELL ADHESION / GRAM POSITIVE PILUS / INTRAMOLECULAR ISOPEPTIDE BOND / INTERNAL THIOESTER
Function / homology
Function and homology information


: / DNA polymerase; domain 1 - #480 / Thioester domain / : / Domain of unknown function (DUF7601) / Domain of unknown function (DUF5979) / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain ...: / DNA polymerase; domain 1 - #480 / Thioester domain / : / Domain of unknown function (DUF7601) / Domain of unknown function (DUF5979) / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / DNA polymerase; domain 1 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPointon, J.A. / Smith, W.D. / Saalbach, G. / Crow, A. / Kehoe, M.A. / Banfield, M.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A Highly Unusual Thioester Bond in a Pilus Adhesin is Required for Efficient Host Cell Interaction
Authors: Pointon, J.A. / Smith, W.D. / Saalbach, G. / Crow, A. / Kehoe, M.A. / Banfield, M.J.
History
DepositionJun 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: ANCILLARY PROTEIN 1
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)102,9512
Polymers102,9512
Non-polymers00
Water9,494527
1
A: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,4751
Polymers51,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,4751
Polymers51,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.480, 66.460, 101.800
Angle α, β, γ (deg.)86.06, 90.06, 75.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ANCILLARY PROTEIN 1 / SPY0125 / COLLAGEN BINDING PROTEIN


Mass: 51475.434 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 286-723
Source method: isolated from a genetically manipulated source
Details: INTERNAL THIOESTER LINKAGE BETWEEN CYS426 AND GLN575. INTRAMOLECULAR ISOPEPTIDE BOND BETWEEN LYS297 AND ASP595. INTRAMOLECULAR ISOPEPTIDE BOND BETWEEN LYS610 AND ASN715.
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: SF370 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GRA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5.75
Details: 38 - 40 % PEG 4000, 200 MM SODIUM ACETATE AND 100 MM TRI-SODIUM CITRATE PH 5.6 - 5.9; 34 TO 36 % PEG 5000-MME, 100 MM AMMONIUM SULPHATE, 100 MM MES PH 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2009 / Details: MIRROS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→38 Å / Num. obs: 66113 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5 / % possible all: 74.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→34.11 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.937 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CA 120 RESIDUES AT C_TERMINUS ARE DISORDERED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CA 120 RESIDUES AT C_TERMINUS ARE DISORDERED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. ATOM AND ANISO RECORDS BELOW CONTAIN THE SUM OF TLS AND RESIDUAL B/U FACTORS, AS OUPUT FROM REFMAC5 USING THE 'TLSO ADDU' OPTION. WATERS HAVE BEEN INCLUDED IN THE TLS REFINEMENT, BUT TO WHICH GROUP THEY HAVE BEEN ASSIGNED IS UNKNOWN.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3370 5.1 %RANDOM
Rwork0.206 ---
obs0.207 62741 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20.15 Å20.34 Å2
2---0.55 Å2-0.65 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 0 527 5423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225003
X-RAY DIFFRACTIONr_bond_other_d0.0010.023357
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9686779
X-RAY DIFFRACTIONr_angle_other_deg0.87138239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6775610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95125.42238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34115869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2191516
X-RAY DIFFRACTIONr_chiral_restr0.080.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
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_it0.7371.53057
X-RAY DIFFRACTIONr_mcbond_other0.2151.51235
X-RAY DIFFRACTIONr_mcangle_it1.27824964
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23531946
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4934.51815
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 162 -
Rwork0.237 3288 -
obs--66.32 %
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)
13.58550.7811-0.68915.58741.03993.89430.0679-0.5318-0.13290.8135-0.27610.48650.407-0.26360.20830.269-0.06480.05680.2976-0.01690.1209-2.1407-14.374836.4097
21.76910.19890.13962.1858-0.28632.4219-0.0295-0.00190.1421-0.0458-0.007-0.0254-0.08590.04650.03650.00960.0055-0.00140.0117-0.00420.06974.8092-3.967112.0493
33.8379-0.37050.82235.19730.83563.67910.0630.62920.1735-0.7624-0.24970.4828-0.3907-0.2520.18660.26450.0649-0.04570.3374-0.00570.1394-2.857337.8996-18.8411
41.7713-0.3783-0.14962.0513-0.31752.2799-0.02170.0328-0.13260.04080.0021-0.00650.0630.05240.01960.0122-0.00930.0020.0149-0.00250.05684.388327.5155.8847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A291 - 387
2X-RAY DIFFRACTION1A586 - 603
3X-RAY DIFFRACTION2A388 - 585
4X-RAY DIFFRACTION3B291 - 387
5X-RAY DIFFRACTION3B586 - 603
6X-RAY DIFFRACTION4B388 - 585

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