PDB-2xic: Pilus-presented adhesin, Spy0125 (Cpa), P212121 form (ESRF data)

ID or keywords:

Entry

Database: PDB / ID: 2xic

Title

Pilus-presented adhesin, Spy0125 (Cpa), P212121 form (ESRF data)

Components

ANCILLARY PROTEIN 1

Keywords

CELL ADHESION / GRAM POSITIVE PILUS / ADHESIN / INTRAMOLECULAR ISOPEPTIDE BOND / INTERNAL THIOESTER

Function / homology

Function and homology information

membrane
Similarity search - Function

Biological species

STREPTOCOCCUS PYOGENES (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Pointon, J.A. / Smith, W.D. / Saalbach, G. / Crow, A. / Kehoe, M.A. / Banfield, M.J.

Citation

Journal: 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

Deposition	Jun 28, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 4, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 30, 2019	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2xic.cif.gz	345.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2xic.ent.gz	293.1 KB	Display	PDB format
PDBx/mmJSON format	2xic.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xi/2xic ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xic	HTTPS FTP

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Related structure data

Related structure data	2xi9C 2xidC C: citing same article (ref.)
Similar structure data	4g83-d 3zg8-d 5nu1-d 3zga-d 5kdn-d 5bua-1 3f8t-d 6xsx-d 1ihg-d 5jly-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ANCILLARY PROTEIN 1

B: ANCILLARY PROTEIN 1

103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ANCILLARY PROTEIN 1

defined by author&software
51.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ANCILLARY PROTEIN 1

defined by author&software
51.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.100, 113.320, 175.360
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	290 - 314
2	1	1	2	B	290 - 314
1	2	1	2	A	324 - 348
2	2	1	2	B	324 - 348
1	3	1	2	A	350 - 357
2	3	1	2	B	350 - 357
1	4	1	2	A	359 - 370
2	4	1	2	B	359 - 370
1	5	1	2	A	379 - 387
2	5	1	2	B	379 - 387
1	6	1	2	A	582 - 596
2	6	1	2	B	582 - 596
1	1	2	2	A	388 - 397
2	1	2	2	B	388 - 397
1	2	2	2	A	399 - 437
2	2	2	2	B	399 - 437
1	3	2	2	A	439 - 580
2	3	2	2	B	439 - 580
1	1	3	2	A	604 - 608
2	1	3	2	B	604 - 608
1	2	3	2	A	610 - 641
2	2	3	2	B	610 - 641
1	3	3	2	A	643 - 657
2	3	3	2	B	643 - 657
1	4	3	2	A	659 - 696
2	4	3	2	B	659 - 696
1	5	3	2	A	698 - 719
2	5	3	2	B	698 - 719

NCS ensembles :

ID
1
2
3

#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 / Water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O

#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 /

Water

Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.7 % / Description: NONE
Crystal grow	pH: 5.75 Details: 38 - 40 % PEG 4000, 200 MM SODIUM ACETATE AND 100 MM TRI - SODIUM CITRATE PH 5.6 REMARK 280 MM MES PH 6.0 - 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2009 / Details: MIRRORS
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.9→56.66 Å / Num. obs: 19907 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / R_merge(I) obs: 0.11 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX	AUTOSOL	phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.9→95.18 Å / Cor.coef. F_o:F_c: 0.894 / Cor.coef. F_o:F_c free: 0.859 / SU B: 42.857 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.483 / 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 ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	1016	5.1 %	RANDOM
R_work	0.231	-	-	-
obs	0.233	18837	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 40.38 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	0 Å²
2-	-	1.12 Å²	0 Å²
3-	-	-	-1.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→95.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6721	0	0	21	6742

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	6854
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	4599
X-RAY DIFFRACTION	r_angle_refined_deg	0.909	1.967	9276
X-RAY DIFFRACTION	r_angle_other_deg	0.787	3	11312
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.405	5	841
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.837	25.714	322
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.5	15	1221
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.869	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1044
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	7587
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1291
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.082	1.5	4210
X-RAY DIFFRACTION	r_mcbond_other	0.025	1.5	1714
X-RAY DIFFRACTION	r_mcangle_it	0.161	2	6829
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.282	3	2644
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.47	4.5	2447
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	553	tight positional	0.02	0.05
1	2	B	553	tight positional	0.02	0.05
2	1	A	1126	tight positional	0.01	0.05
2	2	B	1126	tight positional	0.01	0.05
3	1	A	662	tight positional	0.01	0.05
3	2	B	662	tight positional	0.01	0.05
1	1	A	696	medium positional	0.01	0.5
1	2	B	696	medium positional	0.01	0.5
2	1	A	1459	medium positional	0.01	0.5
2	2	B	1459	medium positional	0.01	0.5
3	1	A	799	medium positional	0.09	0.5
3	2	B	799	medium positional	0.09	0.5
1	1	A	553	tight thermal	0.02	0.5
1	2	B	553	tight thermal	0.02	0.5
2	1	A	1126	tight thermal	0.02	0.5
2	2	B	1126	tight thermal	0.02	0.5
3	1	A	662	tight thermal	0.02	0.5
3	2	B	662	tight thermal	0.02	0.5
1	1	A	696	medium thermal	0.02	2
1	2	B	696	medium thermal	0.02	2
2	1	A	1459	medium thermal	0.03	2
2	2	B	1459	medium thermal	0.03	2
3	1	A	799	medium thermal	0.02	2
3	2	B	799	medium thermal	0.02	2

LS refinement shell

Resolution: 2.9→2.98 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.41	63	-
R_work	0.309	1358	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.8712	1.0094	-0.2323	4.1416	1.2314	6.6407	0.1962	0.1563	-0.224	0.0184	-0.2976	0.1356	0.704	0.0567	0.1015	0.0956	0.0319	-0.0085	0.0412	-0.0215	0.062	-8.6599	-19.568	20.9132
2	3.5592	-0.7984	1.1504	3.9187	-0.7705	4.5141	0.2259	-0.7224	-0.1427	0.2812	-0.1321	-0.0363	0.1081	0.2025	-0.0938	0.0783	-0.0763	-0.0028	0.2163	0.0363	0.0525	-5.5437	-14.1097	48.4333
3	7.6932	0.3264	-1.5192	4.3058	-0.5069	10.0981	0.0266	0.3612	-0.4356	-0.5114	-0.2902	0.2167	0.4502	-0.1792	0.2636	0.0977	0.03	-0.0624	0.0491	-0.0545	0.1685	17.9234	-17.0799	2.8943
4	1.5767	-1.077	0.1145	5.9498	1.4527	5.4409	0.1767	-0.0458	0.3523	-0.303	-0.1997	0.0795	-0.4841	-0.056	0.023	0.1149	-0.0286	0.022	0.0335	-0.0382	0.2575	-14.6207	17.1442	27.2658
5	2.2232	0.5809	-0.9914	7.3306	2.1912	9.7654	-0.5297	0.5722	0.3414	-1.1187	0.2224	0.9883	-1.0649	0.2998	0.3074	0.3674	-0.204	-0.2187	0.2009	0.141	0.2241	-16.8493	8.2432	3.7937
6	3.2661	-0.1217	0.4854	5.3148	1.7607	10.8687	-0.2266	0.5405	0.7257	-1.3885	0.3371	-0.3944	-2.1763	1.6212	-0.1105	1.1278	-0.8371	-0.0724	0.7876	0.227	0.3065	-6.1307	18.2983	-5.1225
7	9.8718	1.5965	1.8977	3.2643	0.3743	9.732	-0.2581	-0.6469	0.4953	0.4454	-0.0714	0.3443	0.0111	-0.4594	0.3295	0.1137	-0.0047	0.0913	0.0969	-0.1355	0.2812	15.0806	10.2049	46.0198

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	290 - 387
2	X-RAY DIFFRACTION	1	A	586 - 604
3	X-RAY DIFFRACTION	2	A	388 - 585
4	X-RAY DIFFRACTION	3	A	605 - 719
5	X-RAY DIFFRACTION	4	B	287 - 387
6	X-RAY DIFFRACTION	4	B	586 - 604
7	X-RAY DIFFRACTION	5	B	388 - 469
8	X-RAY DIFFRACTION	5	B	563 - 585
9	X-RAY DIFFRACTION	6	B	470 - 562
10	X-RAY DIFFRACTION	7	B	605 - 720

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