PDB-3bnv: Crystal structure of Cj0977, a sigma28-regulated virulence protei...

ID or keywords:

Entry

Database: PDB / ID: 3bnv

Title

Crystal structure of Cj0977, a sigma28-regulated virulence protein from Campylobacter jejuni.

Components

Cj0977

Keywords

UNKNOWN FUNCTION / virulence factor / hot-dog fold / Campylobacter jejuni / flagella

Function / homology

Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Cj0977

Function and homology information

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.6 Å

Authors

Yokoyama, T. / Yeo, H.J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structure of a sigma28-regulated nonflagellar virulence protein from Campylobacter jejuni.
Authors: Yokoyama, T. / Paek, S. / Ewing, C.P. / Guerry, P. / Yeo, H.J.

History

Deposition	Dec 14, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3bnv.cif.gz	217.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3bnv.ent.gz	177.6 KB	Display	PDB format
PDBx/mmJSON format	3bnv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3bnv_validation.pdf.gz	491.4 KB	Display	wwPDB validaton report
Full document	3bnv_full_validation.pdf.gz	534.9 KB	Display
Data in XML	3bnv_validation.xml.gz	48.9 KB	Display
Data in CIF	3bnv_validation.cif.gz	63.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/3bnv ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bnv	HTTPS FTP

-
Related structure data

Similar structure data	1ctu-d 5gto-d 3os3-d 6d0p-3 6nyu-1 5u41-2 2piv-d 7bq3-d 5n51-d 6mbg-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Cj0977

B: Cj0977

C: Cj0977

D: Cj0977

E: Cj0977

F: Cj0977

G: Cj0977

H: Cj0977

137 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cj0977

B: Cj0977

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

2

C: Cj0977

D: Cj0977

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

3

E: Cj0977

F: Cj0977

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

4

G: Cj0977

H: Cj0977

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

Unit cell

Length a, b, c (Å)	79.876, 94.533, 81.818
Angle α, β, γ (deg.)	90.00, 99.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	THR	THR	5	A	A	13 - 31	9 - 27
2	1	GLU	GLU	THR	THR	5	B	B	14 - 31	10 - 27
3	1	LEU	LEU	THR	THR	5	C	C	13 - 31	9 - 27
4	1	GLN	GLN	THR	THR	5	D	D	12 - 31	8 - 27
5	1	LEU	LEU	THR	THR	5	E	E	13 - 31	9 - 27
6	1	LEU	LEU	THR	THR	5	F	F	13 - 31	9 - 27
7	1	VAL	VAL	THR	THR	5	G	G	25 - 31	21 - 27
8	1	ARG	ARG	THR	THR	5	H	H	24 - 31	20 - 27
9	2	CYS	CYS	VAL	VAL	2	A	A	32 - 146	28 - 142
10	2	CYS	CYS	VAL	VAL	2	B	B	32 - 146	28 - 142
11	2	CYS	CYS	VAL	VAL	2	C	C	32 - 146	28 - 142
12	2	CYS	CYS	VAL	VAL	2	D	D	32 - 146	28 - 142
13	2	CYS	CYS	VAL	VAL	2	E	E	32 - 146	28 - 142
14	2	CYS	CYS	VAL	VAL	2	F	F	32 - 146	28 - 142
15	2	CYS	CYS	VAL	VAL	2	G	G	32 - 146	28 - 142
16	2	CYS	CYS	VAL	VAL	2	H	H	32 - 146	28 - 142
17	3	SER	SER	LYS	LYS	5	A	A	147 - 154	143 - 150
18	3	SER	SER	LEU	LEU	5	B	B	147 - 155	143 - 151
19	3	SER	SER	LYS	LYS	5	C	C	147 - 154	143 - 150
20	3	SER	SER	LYS	LYS	5	D	D	147 - 154	143 - 150
21	3	SER	SER	LYS	LYS	5	E	E	147 - 154	143 - 150
22	3	SER	SER	LYS	LYS	5	F	F	147 - 154	143 - 150
23	3	SER	SER	LYS	LYS	5	G	G	147 - 154	143 - 150
24	3	SER	SER	PHE	PHE	5	H	H	147 - 153	143 - 149

#1: Protein	Cj0977 Mass: 17103.100 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / Gene: cj0977 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q0R4E3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.79 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 26% PEG4000, 0.2M ammonium acetate, 0.1M Tris-HCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 285K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97929,0.979450,0.971620

Detector

Type: SBC3 3k X 3k CCD / Detector: CCD

Radiation

Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97929	1
2	0.97945	1
3	0.97162	1

Reflection

Resolution: 2.6→37.93 Å / Num. obs: 36505 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 6.43 % / R_merge(I) obs: 0.098 / Net I/σ(I): 7.1

Reflection shell

Resolution: 2.6→2.69 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.339 / Num. unique all: 2586 / % possible all: 68.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data collection
HKL-3000		data reduction
SCALEPACK		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.6→37.93 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.862 / SU B: 26.079 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26925	1790	5 %	RANDOM
R_work	0.21306	-	-	-
obs	0.21589	34092	96.79 %	-

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: 33.898 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0.72 Å²
2-	-	-0.22 Å²	0 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→37.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8609	0	0	111	8720

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	8748
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.433	1.963	11809
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.071	5	1095
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.653	25.505	376
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.675	15	1597
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.263	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	1413
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6351
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.275	0.3	3901
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.337	0.5	6179
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.224	0.5	572
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	0.33	0.3	59
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.282	0.5	8
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	0.459	1.5	5587
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.658	2	8861
X-RAY DIFFRACTION	r_scbond_it	1.448	3	3438
X-RAY DIFFRACTION	r_scangle_it	2.103	4.5	2948
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	440	tight positional	0.05	0.05
2	B	440	tight positional	0.05	0.05
3	C	440	tight positional	0.05	0.05
4	D	440	tight positional	0.05	0.05
5	E	440	tight positional	0.05	0.05
6	F	440	tight positional	0.05	0.05
7	G	440	tight positional	0.04	0.05
8	H	440	tight positional	0.05	0.05
1	A	460	medium positional	0.65	0.5
2	B	460	medium positional	0.73	0.5
3	C	460	medium positional	0.79	0.5
4	D	460	medium positional	0.7	0.5
5	E	460	medium positional	0.77	0.5
6	F	460	medium positional	0.72	0.5
7	G	460	medium positional	0.83	0.5
8	H	460	medium positional	0.81	0.5
1	A	58	loose positional	1.39	5
2	B	58	loose positional	1.23	5
3	C	58	loose positional	1.21	5
4	D	58	loose positional	1.08	5
5	E	58	loose positional	1.6	5
6	F	58	loose positional	1.25	5
7	G	58	loose positional	1.53	5
8	H	58	loose positional	2.85	5
1	A	440	tight thermal	0.09	0.5
2	B	440	tight thermal	0.09	0.5
3	C	440	tight thermal	0.08	0.5
4	D	440	tight thermal	0.09	0.5
5	E	440	tight thermal	0.07	0.5
6	F	440	tight thermal	0.08	0.5
7	G	440	tight thermal	0.06	0.5
8	H	440	tight thermal	0.08	0.5
1	A	460	medium thermal	0.71	2
2	B	460	medium thermal	0.69	2
3	C	460	medium thermal	0.59	2
4	D	460	medium thermal	0.82	2
5	E	460	medium thermal	0.56	2
6	F	460	medium thermal	0.56	2
7	G	460	medium thermal	0.51	2
8	H	460	medium thermal	0.6	2
1	A	58	loose thermal	2.03	10
2	B	58	loose thermal	2.46	10
3	C	58	loose thermal	1.26	10
4	D	58	loose thermal	2.85	10
5	E	58	loose thermal	1.35	10
6	F	58	loose thermal	1.29	10
7	G	58	loose thermal	1.76	10
8	H	58	loose thermal	2.02	10

LS refinement shell

Resolution: 2.6→2.668 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.455	90	-
R_work	0.418	1940	-
obs	-	-	74.39 %

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	6.6509	-0.3764	-2.214	2.6723	0.2915	3.3754	0.2406	-0.7517	0.4367	0.1325	0.0269	0.1585	-0.1971	0.2172	-0.2675	-0.2193	-0.0195	-0.0207	-0.1893	-0.0666	-0.2121	13.8675	7.6759	29.9336
2	6.9488	0.0651	-1.7704	2.4443	0.334	2.832	-0.3444	0.1541	-1.5012	-0.1323	0.0252	0.1064	0.58	0.0583	0.3191	-0.0861	-0.0001	-0.0173	-0.2236	-0.0684	0.0604	18.3918	-9.839	19.5682
3	5.2623	-0.4241	3.0471	2.8909	-0.1744	6.5983	0.3511	0.1303	-0.9144	0.0736	0.0312	-0.2897	1.3268	0.8579	-0.3823	0.047	0.2424	-0.0337	-0.0515	-0.006	-0.1005	15.4101	14.6615	65.8215
4	4.5008	-0.3994	1.922	2.6867	-0.4065	5.2623	-0.2911	0.1186	0.3613	-0.0019	0.0334	0.1111	-0.3299	0.0885	0.2577	-0.1986	-0.0245	-0.0426	-0.2161	0.0416	-0.2827	4.2612	31.6493	60.187
5	6.3123	-2.3221	-2.142	6.3035	1.3678	2.9846	0.1229	-0.0551	1.0815	-0.1755	0.3324	-0.6542	-0.8264	0.1741	-0.4553	0.0748	-0.0323	0.0623	-0.1589	-0.0233	-0.0114	3.9996	48.227	98.5085
6	7.1499	-2.8921	-1.9873	6.2955	1.0887	2.6999	-0.3135	0.2745	-1.1424	0.2469	0.1013	1.3509	0.0338	-0.281	0.2122	-0.1846	0.0039	0.0956	-0.1425	0.0468	0.123	-6.5732	29.9995	98.2783
7	4.3177	0.2519	0.7773	5.0537	0.2124	5.364	-0.1072	-0.2668	1.5461	0.2847	0.3153	0.4698	-1.3353	-0.5787	-0.2081	0.2683	0.2432	0.1648	0.0251	-0.0371	0.6242	12.2364	70.9146	61.7903
8	5.3544	0.7817	5.3644	3.6552	1.0281	13.4344	0.0519	0.1277	0.4524	-0.229	0.2156	0.0621	-0.1516	-0.3199	-0.2675	-0.215	0.0372	0.021	-0.1461	0.0923	-0.0628	15.1096	54.2386	52.4011

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	13 - 154	9 - 150
2	X-RAY DIFFRACTION	2	B	B	14 - 155	10 - 151
3	X-RAY DIFFRACTION	3	C	C	13 - 154	9 - 150
4	X-RAY DIFFRACTION	4	D	D	12 - 154	8 - 150
5	X-RAY DIFFRACTION	5	E	E	13 - 154	9 - 150
6	X-RAY DIFFRACTION	6	F	F	13 - 154	9 - 150
7	X-RAY DIFFRACTION	7	G	G	25 - 154	21 - 150
8	X-RAY DIFFRACTION	8	H	H	24 - 153	20 - 149

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi