PDB-8f90: Intramolecular ester bond-containing repeat domain 2 from Suiprao...

ID or keywords:

Entry

Database: PDB / ID: 8f90

Title

Intramolecular ester bond-containing repeat domain 2 from Suipraoptans intestinalis adhesin

Components

Adhesin

Keywords

CELL ADHESION / bacterial adhesin domain / Ig-like domain / intramolecular ester bond

Function / homology

Function and homology information

extracellular region / metal ion binding / membrane
Similarity search - Function

Biological species

Suipraeoptans intestinalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Jin, S. / Young, P.G. / Squire, C.J.

Funding support

1items

Citation

Journal: To Be Published
Title: Intramolecular ester bond-containing repeat domain from Suipraoptans intestinalis adhesin
Authors: Jin, S. / Young, P.G. / Squire, C.J.

History

Deposition	Nov 22, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8f90.cif.gz	228.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8f90.ent.gz	178.9 KB	Display	PDB format
PDBx/mmJSON format	8f90.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8f90_validation.pdf.gz	425.5 KB	Display	wwPDB validaton report
Full document	8f90_full_validation.pdf.gz	425.7 KB	Display
Data in XML	8f90_validation.xml.gz	25.8 KB	Display
Data in CIF	8f90_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/8f90 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f90	HTTPS FTP

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Related structure data

Related structure data	8fhaC 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

Deposited unit

A: Adhesin

B: Adhesin

C: Adhesin

D: Adhesin

hetero molecules

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

1

A: Adhesin

hetero molecules

defined by author&software
Evidence: gel filtration
15.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Adhesin

hetero molecules

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

3

C: Adhesin

hetero molecules

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

4

D: Adhesin

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.075, 90.603, 89.686
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Adhesin / VaFE repeat-containing surface-anchored protein Mass: 15873.245 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Suipraeoptans intestinalis (bacteria) / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N7UZI9
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.63 Å³/Da / Density % sol: 53.16 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953739 Å / Relative weight: 1
Reflection	Resolution: 1.46→45.301 Å / Num. obs: 114397 / % possible obs: 99.6 % / Redundancy: 13.6 % / CC_1/2: 0.999 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.46→1.49 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5159 / CC_1/2: 0.211 / % possible all: 92.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→45.301 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.192 / WR_factor R_work: 0.151 / SU B: 3.864 / SU ML: 0.058 / Average fsc free: 0.9143 / Average fsc work: 0.9296 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1981	4410	4.969 %	random selection
R_work	0.1572	84347	-	-
all	0.159	-	-	-
obs	-	88757	99.972 %	-

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: 22.769 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.317 Å²	0 Å²	-0 Å²
2-	-	0.135 Å²	0 Å²
3-	-	-	0.182 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→45.301 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4346	0	4	459	4809

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	4482
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	4087
X-RAY DIFFRACTION	r_angle_refined_deg	1.279	1.658	6101
X-RAY DIFFRACTION	r_angle_other_deg	1.304	1.58	9500
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.113	5	600
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.77	26.284	183
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.419	15	695
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.711	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	639
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5141
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	831
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	597
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.171	0.2	3663
X-RAY DIFFRACTION	r_nbtor_refined	0.146	0.2	2097
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	2008
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	292
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	63
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.089	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.478	2.187	2382
X-RAY DIFFRACTION	r_mcbond_other	1.447	2.185	2381
X-RAY DIFFRACTION	r_mcangle_it	1.879	3.287	2976
X-RAY DIFFRACTION	r_mcangle_other	1.883	3.288	2977
X-RAY DIFFRACTION	r_scbond_it	2.003	2.517	2100
X-RAY DIFFRACTION	r_scbond_other	2.001	2.518	2097
X-RAY DIFFRACTION	r_scangle_it	2.485	3.641	3121
X-RAY DIFFRACTION	r_scangle_other	2.484	3.641	3122
X-RAY DIFFRACTION	r_lrange_it	2.928	27.002	4555
X-RAY DIFFRACTION	r_lrange_other	2.834	26.709	4498
X-RAY DIFFRACTION	r_rigid_bond_restr	0.984	3	8569

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.6-1.642	0.299	357	0.283	6128	0.284	6493	0.769	0.772	99.8768	0.246
1.642-1.686	0.305	373	0.251	5943	0.254	6319	0.773	0.806	99.9525	0.215
1.686-1.735	0.271	308	0.213	5813	0.216	6124	0.855	0.87	99.951	0.174
1.735-1.789	0.213	312	0.167	5685	0.17	5999	0.918	0.926	99.9667	0.133
1.789-1.847	0.206	280	0.147	5521	0.15	5801	0.937	0.946	100	0.118
1.847-1.912	0.189	286	0.138	5320	0.141	5606	0.945	0.956	100	0.11
1.912-1.984	0.188	240	0.127	5163	0.13	5404	0.954	0.964	99.9815	0.105
1.984-2.065	0.18	246	0.126	4992	0.129	5239	0.954	0.967	99.9809	0.107
2.065-2.156	0.206	239	0.128	4773	0.131	5012	0.948	0.967	100	0.112
2.156-2.261	0.17	265	0.131	4562	0.133	4827	0.961	0.967	100	0.116
2.261-2.383	0.19	208	0.139	4359	0.141	4567	0.956	0.967	100	0.124
2.383-2.527	0.222	219	0.147	4127	0.151	4346	0.95	0.962	100	0.135
2.527-2.701	0.206	192	0.146	3893	0.149	4085	0.956	0.966	100	0.138
2.701-2.917	0.185	152	0.152	3680	0.153	3832	0.958	0.965	100	0.149
2.917-3.194	0.197	179	0.159	3336	0.161	3515	0.954	0.964	100	0.159
3.194-3.569	0.2	150	0.17	3059	0.171	3209	0.96	0.962	100	0.176
3.569-4.117	0.198	127	0.165	2742	0.166	2869	0.962	0.967	100	0.177
4.117-5.031	0.145	146	0.138	2277	0.139	2423	0.979	0.979	100	0.16
5.031-7.072	0.199	84	0.167	1843	0.169	1927	0.971	0.973	100	0.187
7.072-45.301	0.216	46	0.19	1113	0.191	1161	0.953	0.971	99.8277	0.205

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