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- PDB-2xid: Pilus-presented adhesin, Spy0125 (Cpa), P212121 form (DLS) -

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Basic information

Entry
Database: PDB / ID: 2xid
TitlePilus-presented adhesin, Spy0125 (Cpa), P212121 form (DLS)
ComponentsANCILLARY PROTEIN 1
KeywordsCELL ADHESION / GRAM POSITIVE PILUS / ADHESIN / INTRAMOLECULAR ISOPEPTIDE BOND / INTERNAL THIOESTER
Function / homology
Function and homology information


DNA polymerase; domain 1 - #480 / Thioester domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain ...DNA polymerase; domain 1 - #480 / Thioester domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 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 1.4Dec 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Jun 12, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANCILLARY PROTEIN 1
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)102,5762
Polymers102,5762
Non-polymers00
Water41423
1
A: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,2881
Polymers51,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,2881
Polymers51,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.810, 117.500, 177.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLEULEUAA290 - 31424 - 48
211THRTHRLEULEUBB290 - 31424 - 48
121ALAALALEULEUAA324 - 34858 - 82
221ALAALALEULEUBB324 - 34858 - 82
131SERSERALAALAAA350 - 35784 - 91
231SERSERALAALABB350 - 35784 - 91
141PROPROTYRTYRAA359 - 37093 - 104
241PROPROTYRTYRBB359 - 37093 - 104
151GLUGLUGLUGLUAA379 - 387113 - 121
251GLUGLUGLUGLUBB379 - 387113 - 121
161LEULEULYSLYSAA587 - 596321 - 330
261LEULEULYSLYSBB587 - 596321 - 330
112PROPROPHEPHEAA388 - 397122 - 131
212PROPROPHEPHEBB388 - 397122 - 131
122GLUGLUSERSERAA399 - 437133 - 171
222GLUGLUSERSERBB399 - 437133 - 171
132ASPASPTHRTHRAA439 - 580173 - 314
232ASPASPTHRTHRBB439 - 580173 - 314
113ASNASNLEULEUAA605 - 608339 - 342
213ASNASNLEULEUBB605 - 608339 - 342
123LYSLYSVALVALAA610 - 641344 - 375
223LYSLYSVALVALBB610 - 641344 - 375
133THRTHRILEILEAA643 - 657377 - 391
233THRTHRILEILEBB643 - 657377 - 391
143LEULEUALAALAAA659 - 696393 - 430
243LEULEUALAALABB659 - 696393 - 430
153ALAALAPROPROAA698 - 719432 - 453
253ALAALAPROPROBB698 - 719432 - 453

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 51287.855 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.: 23 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growpH: 5.75
Details: 38-40% PEG-4000, 200 MM SODIUM ACETATE, 100 MM TRISODIUM CITRATE PH 5.6-5.9; 34-36% PEG-5000MME, 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: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.65→55 Å / Num. obs: 28853 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 16.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 17.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 8.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XIC

2xic


Resolution: 2.65→98.06 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 32.346 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 3.921 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM AND ANISO RECORDS BELOW CONTAIN THE SUM OF TLS AND RESIDUAL B/U FACTORS, AS OUPUT FROM REFMAC USING THE 'TLSO ADDU' OPTION. WATERS HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM AND ANISO RECORDS BELOW CONTAIN THE SUM OF TLS AND RESIDUAL B/U FACTORS, AS OUPUT FROM REFMAC 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
Rfree0.265 1446 5.1 %RANDOM
Rwork0.227 ---
obs0.229 27150 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.84 Å2
Baniso -1Baniso -2Baniso -3
1-7.45 Å20 Å20 Å2
2---1.68 Å20 Å2
3----5.77 Å2
Refinement stepCycle: LAST / Resolution: 2.65→98.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 0 23 6734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226856
X-RAY DIFFRACTIONr_bond_other_d0.0020.024605
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9669278
X-RAY DIFFRACTIONr_angle_other_deg0.911311328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11125.798326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.152151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.841520
X-RAY DIFFRACTIONr_chiral_restr0.0860.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027607
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021291
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_it0.3881.54209
X-RAY DIFFRACTIONr_mcbond_other0.0981.51716
X-RAY DIFFRACTIONr_mcangle_it0.73626823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23732647
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0844.52453
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A524tight positional0.040.05
12B524tight positional0.040.05
21A1126tight positional0.050.05
22B1126tight positional0.050.05
31A656tight positional0.030.05
32B656tight positional0.030.05
11A644medium positional0.060.5
12B644medium positional0.060.5
21A1459medium positional0.050.5
22B1459medium positional0.050.5
31A789medium positional0.030.5
32B789medium positional0.030.5
11A524tight thermal0.080.5
12B524tight thermal0.080.5
21A1126tight thermal0.110.5
22B1126tight thermal0.110.5
31A656tight thermal0.050.5
32B656tight thermal0.050.5
11A644medium thermal0.092
12B644medium thermal0.092
21A1459medium thermal0.122
22B1459medium thermal0.122
31A789medium thermal0.052
32B789medium thermal0.052
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 112 -
Rwork0.348 1947 -
obs--97.86 %
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)
12.44240.391.04267.87291.131912.8365-0.31320.11550.4056-0.91290.04640.2448-1.2688-0.74550.26690.99710.1764-0.00740.50.08250.3948-12.741120.427920.3687
21.8408-0.4226-1.28972.32140.31057.48540.15370.0810.1484-0.3922-0.05740.13250.5679-0.8436-0.09630.4553-0.0776-0.00050.2868-0.02530.3101-17.475413.774847.9184
310.67612.2595-0.51411.73561.278913.3901-0.65860.66840.2052-1.60980.2432-1.6928-1.40530.73560.41541.5972-0.38280.3860.44270.08140.6795-42.566916.83532.289
42.5812-0.90130.93896.9253-2.42226.9246-0.1564-0.1258-0.26780.48790.36040.6226-0.2146-0.5706-0.2040.19280.05620.07250.29150.03280.3726-7.1352-18.380626.5532
51.69550.54890.81693.39480.10196.2177-0.02160.0514-0.0039-0.14290.08380.0627-0.6073-0.0822-0.06220.0690.01510.00590.17230.01670.2891-8.8916-13.985-1.7667
68.80810.3703-0.03243.68692.5658.7493-0.6013-0.7086-0.04180.56930.3229-0.3757-0.3980.59170.27850.7820.1244-0.18760.40750.02070.4151-39.4419-10.206744.9559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A290 - 387
2X-RAY DIFFRACTION1A586 - 597
3X-RAY DIFFRACTION2A388 - 585
4X-RAY DIFFRACTION3A605 - 719
5X-RAY DIFFRACTION4B287 - 387
6X-RAY DIFFRACTION4B586 - 604
7X-RAY DIFFRACTION5B388 - 585
8X-RAY DIFFRACTION6B605 - 719

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