PDB-7vcn: Crystal Structure of PitA fragment from pilus islet-2 of Streptoc...

ID or keywords:

Entry

Database: PDB / ID: 7vcn

Title

Crystal Structure of PitA fragment from pilus islet-2 of Streptococcus oralis with Tb-Xo4

Components

(von Willebrand factor type A domain protein) x 2

Keywords

CELL ADHESION / Tip pilin / adhesin / PitA / PI-2 pilus / Streptococcus oralis / isopeptide / CnaA fold / CnaB fold / Crystallophore / Terbium / biofilm / dental plaque

Function / homology

Function and homology information

membrane
Similarity search - Function

Biological species

Streptococcus oralis ATCC 35037 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.343 Å

Authors

Yadav, R.K. / Krishnan, V.

Funding support

India, 1items

Citation

Journal: Febs J. / Year: 2022
Title: New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer.
Authors: Yadav, R.K. / Krishnan, V.

History

Deposition	Sep 3, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7vcn.cif.gz	365.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7vcn.ent.gz	290.2 KB	Display	PDB format
PDBx/mmJSON format	7vcn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vc/7vcn ftp://data.pdbj.org/pub/pdb/validation_reports/vc/7vcn	HTTPS FTP

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Related structure data

Related structure data	7f7yC 7vcrC 7w6bC 7w7iC C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (3) #166 - Oct 2013 Proteasome similarity (3) #55 - Jul 2004 DNA Ligase similarity (2)

Deposited unit

C: von Willebrand factor type A domain protein

A: von Willebrand factor type A domain protein

D: von Willebrand factor type A domain protein

B: von Willebrand factor type A domain protein

hetero molecules

113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: von Willebrand factor type A domain protein

A: von Willebrand factor type A domain protein

hetero molecules

defined by author&software
Evidence: gel filtration
56.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: von Willebrand factor type A domain protein

B: von Willebrand factor type A domain protein

hetero molecules

defined by author&software
56.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.815, 70.288, 82.710
Angle α, β, γ (deg.)	79.883, 86.895, 87.186
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	40 - 821
2	2	1	B	40 - 821

#1: Protein/peptide	von Willebrand factor type A domain protein / PitA Mass: 3376.763 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 70-357 was removed during limited proteolysis treatment. Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria) Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3
#2: Protein	von Willebrand factor type A domain protein / PitA Mass: 52158.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 70-357 was removed during limited proteolysis treatment. Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria) Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3
#3: Chemical	ChemComp-7MT / Tb-Xo4 Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₃N₅O₄Tb
#4: Chemical	ChemComp-TB / TERBIUM(III) ION Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 60.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.2 M ammonium acetate 0.1 M HEPES pH 7.2, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.42379 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.42379 Å / Relative weight: 1
Reflection	Resolution: 2.343→69.235 Å / Num. obs: 38153 / % possible obs: 82.6 % / Redundancy: 5.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.03 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.343→2.608 Å / R_merge(I) obs: 0.552 / Num. unique obs: 1909 / CC_1/2: 0.881 / R_pim(I) all: 0.252

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.343→69.139 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.909 / SU B: 18.323 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.639 / ESU R Free: 0.302 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2396	1787	4.684 %
R_work	0.1942	36366	-
all	0.196	-	-
obs	-	38153	66.425 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 62.857 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.747 Å²	-0.162 Å²	-1.082 Å²
2-	-	-0.291 Å²	0.637 Å²
3-	-	-	-0.327 Å²

Refinement step

Cycle: LAST / Resolution: 2.343→69.139 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7581	0	63	114	7758

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	7784
X-RAY DIFFRACTION	r_angle_refined_deg	1.82	1.665	10533
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.647	5	963
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.611	24.684	380
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.108	15	1402
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.95	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	1059
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5760
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	2583
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	5227
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	252
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.209	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.128	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.226	3.269	3873
X-RAY DIFFRACTION	r_mcangle_it	5.356	4.883	4829
X-RAY DIFFRACTION	r_scbond_it	4.206	3.622	3911
X-RAY DIFFRACTION	r_scangle_it	6.603	5.267	5704
X-RAY DIFFRACTION	r_lrange_it	10.855	61.109	30786
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.13	0.05	14045

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.13009	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.13009	0.05007

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.343-2.404	0.384	7	0.255	203	X-RAY DIFFRACTION	4.9775
2.404-2.47	0.349	28	0.303	338	X-RAY DIFFRACTION	8.8278
2.47-2.541	0.337	29	0.308	535	X-RAY DIFFRACTION	14.1071
2.541-2.62	0.385	50	0.311	888	X-RAY DIFFRACTION	23.9653
2.62-2.705	0.359	63	0.282	1328	X-RAY DIFFRACTION	36.586
2.705-2.8	0.314	98	0.282	2002	X-RAY DIFFRACTION	56.8182
2.8-2.906	0.355	125	0.286	2903	X-RAY DIFFRACTION	86.7125
2.906-3.024	0.315	148	0.26	3168	X-RAY DIFFRACTION	96.9591
3.024-3.159	0.274	145	0.242	3040	X-RAY DIFFRACTION	97.1333
3.159-3.312	0.298	173	0.227	2859	X-RAY DIFFRACTION	97.5233
3.312-3.491	0.278	138	0.215	2758	X-RAY DIFFRACTION	97.7388
3.491-3.703	0.245	118	0.215	2636	X-RAY DIFFRACTION	97.8678
3.703-3.958	0.256	102	0.198	2471	X-RAY DIFFRACTION	98.0564
3.958-4.274	0.222	114	0.167	2305	X-RAY DIFFRACTION	98.2934
4.274-4.681	0.162	110	0.134	2137	X-RAY DIFFRACTION	98.5526
4.681-5.231	0.17	96	0.12	1906	X-RAY DIFFRACTION	98.7179
5.231-6.036	0.199	86	0.153	1704	X-RAY DIFFRACTION	99.1141
6.036-7.382	0.216	60	0.162	1445	X-RAY DIFFRACTION	99.0132
7.382-10.398	0.15	66	0.138	1123	X-RAY DIFFRACTION	99.4979
10.398-69.139	0.195	31	0.175	617	X-RAY DIFFRACTION	99.2343

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	0.6996	0.5629	-0.0864	0.8464	0.3722	0.5129	-0.1239	-0.2682	-0.2927	-0.2556	-0.1205	-0.0826	-0.1421	0.1164	0.2443	0.2815	0.0865	0.1152	0.3031	0.0959	0.3951	-18.522	-20.755	-45.247
2	0.0138	0.0352	0.0741	1.3393	1.5805	2.5579	-0.006	-0.0255	-0.0449	-0.0397	-0.0628	0.0233	-0.1418	-0.0298	0.0688	0.1771	-0.0633	0.0023	0.5627	0.0515	0.2071	-21.7014	-0.7722	-25.3065
3	0.6181	0.1164	-0.2694	1.085	1.0555	1.3926	0.0753	0.1989	0.0412	0.1233	0.0654	-0.16	0.0886	-0.2856	-0.1406	0.2281	-0.0155	0.04	0.5119	0.026	0.2186	-19.0863	12.8851	9.2544
4	0.0154	0.1242	-0.018	1.4834	0.1974	1.634	0.0293	0.0485	-0.0428	0.3984	0.118	-0.4267	-0.5267	-0.718	-0.1473	0.4389	0.2004	-0.0189	0.5601	0.005	0.1702	-25.0121	31.4398	41.0992
5	0.1869	-0.0028	-0.246	0.6871	0.3029	0.4598	0.032	0.0305	0.0244	0.079	0.0026	-0.0571	0.0262	-0.0225	-0.0346	0.3428	0.0148	0.0064	0.2865	-0.029	0.3354	2.055	12.153	-1.187
6	0.1509	0.0858	0.0091	1.0922	1.4597	2.0855	0.0247	0.0143	0.0557	0.0435	-0.0309	-0.0466	0.1223	-0.0776	0.0061	0.3708	-0.0177	0.0403	0.2876	-0.0327	0.2929	9.6419	-11.0382	-19.5048
7	0.317	0.1177	-0.0724	0.7825	0.872	1.1377	0.0657	-0.032	0.0435	0.0095	-0.0194	-0.0137	0.0476	-0.0436	-0.0463	0.3725	0.0367	0.0291	0.2779	-0.0422	0.3079	9.7786	-24.956	-54.0289
8	0.0174	0.1136	-0.0408	1.8775	-0.4571	1.267	-0.0144	-0.0284	0.0457	-0.2341	0.0811	-0.0549	0.2176	-0.085	-0.0668	0.3987	-0.0089	0.0171	0.2836	-0.0432	0.3057	1.9871	-44.686	-85.7095

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	C	40 - 69
2	X-RAY DIFFRACTION	1	ALL	B	358 - 499
3	X-RAY DIFFRACTION	2	ALL	B	500 - 604
4	X-RAY DIFFRACTION	3	ALL	B	605 - 710
5	X-RAY DIFFRACTION	4	ALL	B	711 - 821
6	X-RAY DIFFRACTION	5	ALL	D	40 - 69
7	X-RAY DIFFRACTION	5	ALL	A	358 - 499
8	X-RAY DIFFRACTION	6	ALL	A	500 - 604
9	X-RAY DIFFRACTION	7	ALL	A	605 - 710
10	X-RAY DIFFRACTION	8	ALL	A	711 - 823

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