PDB-3bjq: CRYSTAL STRUCTURE OF A PHAGE-RELATED PROTEIN (BB3626) FROM BORDET...

ID or keywords:

Entry

Database: PDB / ID: 3bjq

Title

CRYSTAL STRUCTURE OF A PHAGE-RELATED PROTEIN (BB3626) FROM BORDETELLA BRONCHISEPTICA RB50 AT 2.05 A RESOLUTION

Components

Phage-related protein

Keywords

VIRAL PROTEIN / PHAGE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

phage-related protein like fold / phage-related protein like domain / Major capsid protein GpE / Phage major capsid protein E / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein / Uncharacterized protein

Function and homology information

Biological species

Bordetella bronchiseptica RB50 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.05 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of phage-related protein (NP_890161.1) from Bordetella bronchiseptica at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Dec 4, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 7, 2011	Group: Other
Revision 1.3	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bjq.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3bjq.ent.gz	971.7 KB	Display	PDB format
PDBx/mmJSON format	3bjq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bjq_validation.pdf.gz	522.3 KB	Display	wwPDB validaton report
Full document	3bjq_full_validation.pdf.gz	546.8 KB	Display
Data in XML	3bjq_validation.xml.gz	116.1 KB	Display
Data in CIF	3bjq_validation.cif.gz	162.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjq ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjq	HTTPS FTP

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Related structure data

Similar structure data	20659 5jmn-d 6q4o-d 4dej-d 21447 0784 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 373379

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phage-related protein

B: Phage-related protein

C: Phage-related protein

D: Phage-related protein

E: Phage-related protein

F: Phage-related protein

G: Phage-related protein

H: Phage-related protein

I: Phage-related protein

J: Phage-related protein

hetero molecules

354 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	93.390, 188.320, 105.150
Angle α, β, γ (deg.)	90.000, 106.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	LYS	A	A	12 - 60	13 - 61
2	1	VAL	LYS	B	B	12 - 60	13 - 61
3	1	VAL	LYS	C	C	12 - 60	13 - 61
4	1	VAL	LYS	D	D	12 - 60	13 - 61
5	1	VAL	LYS	E	E	12 - 60	13 - 61
6	1	VAL	LYS	F	F	12 - 60	13 - 61
7	1	VAL	LYS	G	G	12 - 60	13 - 61
8	1	VAL	LYS	H	H	12 - 60	13 - 61
9	1	VAL	LYS	I	I	12 - 60	13 - 61
10	1	VAL	LYS	J	J	12 - 60	13 - 61
11	2	GLU	CYS	A	A	75 - 189	76 - 190
12	2	GLU	CYS	B	B	75 - 189	76 - 190
13	2	GLU	CYS	C	C	75 - 189	76 - 190
14	2	GLU	CYS	D	D	75 - 189	76 - 190
15	2	GLU	CYS	E	E	75 - 189	76 - 190
16	2	GLU	CYS	F	F	75 - 189	76 - 190
17	2	GLU	CYS	G	G	75 - 189	76 - 190
18	2	GLU	CYS	H	H	75 - 189	76 - 190
19	2	GLU	CYS	I	I	75 - 189	76 - 190
20	2	GLU	CYS	J	J	75 - 189	76 - 190
21	3	ILE	ARG	A	A	209 - 227	210 - 228
22	3	ILE	ARG	B	B	209 - 227	210 - 228
23	3	ILE	ARG	C	C	209 - 227	210 - 228
24	3	ILE	ARG	D	D	209 - 227	210 - 228
25	3	ILE	ARG	E	E	209 - 227	210 - 228
26	3	ILE	ARG	F	F	209 - 227	210 - 228
27	3	ILE	ARG	G	G	209 - 227	210 - 228
28	3	ILE	ARG	H	H	209 - 227	210 - 228
29	3	ILE	ARG	I	I	209 - 227	210 - 228
30	3	ILE	ARG	J	J	209 - 227	210 - 228
31	4	GLY	PRO	A	A	237 - 313	238 - 314
32	4	GLY	PRO	B	B	237 - 313	238 - 314
33	4	GLY	PRO	C	C	237 - 313	238 - 314
34	4	GLY	PRO	D	D	237 - 313	238 - 314
35	4	GLY	PRO	E	E	237 - 313	238 - 314
36	4	GLY	PRO	F	F	237 - 313	238 - 314
37	4	GLY	PRO	G	G	237 - 313	238 - 314
38	4	GLY	PRO	H	H	237 - 313	238 - 314
39	4	GLY	PRO	I	I	237 - 313	238 - 314
40	4	GLY	PRO	J	J	237 - 313	238 - 314

#1: Protein	Phage-related protein Mass: 34941.262 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria) Species: Bordetella bronchiseptica / Strain: RB50 / NCTC 13252 / Gene: NP_890161.1, BB3626 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WDF2, UniProt: A0A0H3LS71*PLUS
#2: Chemical	... ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1336 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)	Description
1	2.54	51.5	THE STRUCTURE WAS SOLVED BY MAD METHOD USING ANOTHER CRYSTAL AT LOWER RESOLUTION. THE CRYSTAL USED FOR REFINEMENT IS NOT ISOMORPHOUS TO THE CRYSTAL USED FOR PHASING. RIGID BODY REFINEMENT OF THE INITIAL MAD MODEL WAS SUFFICIENT TO ORIENT THE MONOMERS IN THE SET USED FOR REFINEMENT.
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
277	1	vapor diffusion, sitting drop	5.79	NANODROP, 25.1% PEG 200, 5.0% PEG 3000, 0.1M MES pH 5.79, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277	2	vapor diffusion, sitting drop	6	NANODROP, 30.0% PEG 200, 5.0% PEG 3000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-D	1	0.9184
SYNCHROTRON	SSRL	BL11-1	2	0.97916, 0.91162

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 300 mm CCD	1	CCD	Oct 25, 2007	Adjustable focusing mirrors in K-B geometry
MARMOSAIC 325 mm CCD	2	CCD	Apr 9, 2007	Flat mirror (vertical focusing)

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111) Double crystal	SINGLE WAVELENGTH	M	x-ray	1
2	Single crystal Si(111) bent (horizontal focusing)	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9184	1
2	0.97916	1
3	0.91162	1

Reflection

Resolution: 2.05→49.147 Å / Num. obs: 216795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.49 % / B_iso Wilson estimate: 33.52 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 11.24

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.05-2.08	3.78	0.847	1.7	34704	9184	99.3
2.08-2.15		0.712	1.9	74779	19575	99.8
2.15-2.24		0.58	2.4	83063	21729	99.8
2.24-2.34		0.463	3	77523	20338	99.6
2.34-2.47		0.342	4	83466	21757	99.8
2.47-2.62		0.258	5.2	77071	20062	99.8
2.62-2.82		0.3	7.6	121653	20550	99.8
2.82-3.1		0.227	11.3	154602	20614	99.8
3.1-3.55		0.114	18.4	161091	20939	99.8
3.55-4.47		0.058	27.9	161250	20942	99.8
4.47-49.147		0.046	34.1	160172	21105	99.7

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
XDS		data reduction
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.05→49.147 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.941 / SU B: 9.972 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.227	3532	1.6 %	THIN SHELLS
R_work	0.186	-	-	-
obs	0.186	216789	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 43.017 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.64 Å²	0 Å²	0.1 Å²
2-	-	-1.2 Å²	0 Å²
3-	-	-	-0.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→49.147 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22752	0	262	1336	24350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	23670
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	16050
X-RAY DIFFRACTION	r_angle_refined_deg	1.399	1.975	32156
X-RAY DIFFRACTION	r_angle_other_deg	0.892	3	39238
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.751	5	2983
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.124	23.992	967
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.783	15	3724
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.565	15	134
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	3556
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	26153
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4549
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	4583
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	16385
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	11427
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	12349
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	1368
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.073	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.216	0.2	68
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.213	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.491	3	15298
X-RAY DIFFRACTION	r_mcbond_other	0.417	3	5976
X-RAY DIFFRACTION	r_mcangle_it	2.337	5	23943
X-RAY DIFFRACTION	r_scbond_it	4.244	8	9720
X-RAY DIFFRACTION	r_scangle_it	5.874	11	8193

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	1497	TIGHT POSITIONAL	0.1	0.1
2	B	1497	TIGHT POSITIONAL	0.13	0.1
3	C	1497	TIGHT POSITIONAL	0.09	0.1
4	D	1497	TIGHT POSITIONAL	0.12	0.1
5	E	1497	TIGHT POSITIONAL	0.1	0.1
6	F	1497	TIGHT POSITIONAL	0.1	0.1
7	G	1497	TIGHT POSITIONAL	0.11	0.1
8	H	1497	TIGHT POSITIONAL	0.1	0.1
9	I	1497	TIGHT POSITIONAL	0.09	0.1
10	J	1497	TIGHT POSITIONAL	0.16	0.1
1	A	1689	MEDIUM POSITIONAL	0.3	0.5
2	B	1689	MEDIUM POSITIONAL	0.35	0.5
3	C	1689	MEDIUM POSITIONAL	0.32	0.5
4	D	1689	MEDIUM POSITIONAL	0.34	0.5
5	E	1689	MEDIUM POSITIONAL	0.37	0.5
6	F	1689	MEDIUM POSITIONAL	0.34	0.5
7	G	1689	MEDIUM POSITIONAL	0.29	0.5
8	H	1689	MEDIUM POSITIONAL	0.38	0.5
9	I	1689	MEDIUM POSITIONAL	0.31	0.5
10	J	1689	MEDIUM POSITIONAL	0.39	0.5
1	A	1497	TIGHT THERMAL	0.53	1.2
2	B	1497	TIGHT THERMAL	0.48	1.2
3	C	1497	TIGHT THERMAL	0.38	1.2
4	D	1497	TIGHT THERMAL	0.5	1.2
5	E	1497	TIGHT THERMAL	0.49	1.2
6	F	1497	TIGHT THERMAL	0.41	1.2
7	G	1497	TIGHT THERMAL	0.48	1.2
8	H	1497	TIGHT THERMAL	0.45	1.2
9	I	1497	TIGHT THERMAL	0.43	1.2
10	J	1497	TIGHT THERMAL	0.54	1.2
1	A	1689	MEDIUM THERMAL	1.39	3
2	B	1689	MEDIUM THERMAL	1.36	3
3	C	1689	MEDIUM THERMAL	1.21	3
4	D	1689	MEDIUM THERMAL	1.4	3
5	E	1689	MEDIUM THERMAL	1.31	3
6	F	1689	MEDIUM THERMAL	1.22	3
7	G	1689	MEDIUM THERMAL	1.36	3
8	H	1689	MEDIUM THERMAL	1.25	3
9	I	1689	MEDIUM THERMAL	1.22	3
10	J	1689	MEDIUM THERMAL	1.44	3

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	276	-
R_work	0.277	15688	-
all	-	15964	-
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	0.5453	-0.0691	-0.3092	0.4635	0.5187	1.4497	0.0008	-0.0676	0.0253	0.1505	-0.0404	0.0677	0.2283	-0.1791	0.0396	-0.078	-0.0279	-0.0168	-0.0411	-0.0254	-0.0688	-101.7376	77.1966	-10.1837
2	1.0457	0.3876	0.1132	0.6274	0.0651	0.8725	-0.0138	-0.0337	0.058	0.0744	0.0242	0.0142	0.0987	-0.0938	-0.0104	-0.0194	-0.0397	0.0233	-0.109	0.0227	-0.0996	-93.9595	39.3774	28.706
3	0.9405	-0.1565	0.9186	0.7034	-0.5607	2.4765	-0.0805	0.2961	-0.2061	-0.0359	0.0339	0.0594	0.1107	0.0549	0.0466	-0.0507	-0.0723	0.08	0.1114	-0.1157	0.0367	-116.2426	61.2903	15.5133
4	0.4032	-0.0638	0.2315	1.0701	-0.2824	0.4173	-0.0423	-0.0248	0.0451	-0.13	0.0074	-0.2068	0.1032	-0.0114	0.0348	-0.0893	-0.013	0.0661	-0.109	-0.0122	-0.062	-70.7435	65.3526	-12.3932
5	0.0987	-0.094	0.016	0.4347	-0.2283	0.6275	0.0439	-0.0392	-0.0514	0.0554	-0.0329	-0.2012	0.1557	0.0684	-0.011	-0.055	-0.0105	-0.0098	-0.0973	0.0008	-0.0122	-66.0478	42.1311	12.3116
6	1.5692	-0.695	0.3113	1.2177	-0.5356	0.2827	-0.122	0.0016	0.1571	0.3848	0.007	-0.1872	-0.2575	0.0971	0.115	0.0666	-0.0694	-0.0379	0.0156	0.0739	0.0091	-86.8069	87.8544	65.9634
7	1.2641	0.3403	-0.1487	0.673	-0.051	0.635	0.0591	0.0081	-0.0318	0.0953	-0.0457	0.0178	-0.133	0.0048	-0.0135	-0.0457	-0.0261	-0.0515	-0.0504	-0.0182	-0.0688	-55.1328	81.8907	57.9547
8	1.4078	-0.629	-0.2134	0.677	0.0889	0.4594	-0.0785	-0.0319	-0.0093	0.1895	0.0835	-0.0325	-0.0276	0.0521	-0.005	0.0155	0.0279	-0.0019	-0.0879	-0.0141	-0.0776	-72.8221	119.2365	22.6587
9	0.1131	-0.1581	0.1206	0.4949	0.0623	0.8708	0.0026	0.0026	0.0268	-0.062	0.0636	-0.04	-0.1476	0.0218	-0.0661	-0.0533	-0.0198	0.0128	-0.0261	-0.0504	0.0094	-45.7337	101.3366	31.2229
10	0.2907	0.0225	0.1658	0.9791	0.3959	1.5762	0.0082	-0.0667	-0.0199	0.0426	0.1022	-0.0165	0.045	-0.0231	-0.1104	-0.0861	0.0469	0.0264	-0.0731	-0.0097	-0.1018	-97.5631	112.1943	43.8828

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	8 - 314	9 - 315
2	X-RAY DIFFRACTION	2	B	B	8 - 314	9 - 315
3	X-RAY DIFFRACTION	3	C	C	8 - 314	9 - 315
4	X-RAY DIFFRACTION	4	D	D	8 - 315	9 - 316
5	X-RAY DIFFRACTION	5	E	E	8 - 315	9 - 316
6	X-RAY DIFFRACTION	6	F	F	8 - 315	9 - 316
7	X-RAY DIFFRACTION	7	G	G	8 - 315	9 - 316
8	X-RAY DIFFRACTION	8	H	H	8 - 314	9 - 315
9	X-RAY DIFFRACTION	9	I	I	8 - 315	9 - 316
10	X-RAY DIFFRACTION	10	J	J	8 - 315	9 - 316

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