PDB-3kk4: uncharacterized protein BP1543 from Bordetella pertussis Tohama I

ID or keywords:

Entry

Database: PDB / ID: 3kk4

Title

uncharacterized protein BP1543 from Bordetella pertussis Tohama I

Components

uncharacterized protein BP1543

Keywords

structural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Ribbon-helix-helix fold / protein bp1543 / Ribbon-helix-helix domain / Ribbon-helix-helix domain superfamily / Ribbon-helix-helix domain / Orthogonal Bundle / Mainly Alpha / ACETATE ION / Ribbon-helix-helix domain-containing protein

Function and homology information

Biological species

Bordetella pertussis Tohama I (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Chang, C. / Chhor, G. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of uncharacterized protein BP1543 from Bordetella pertussis Tohama I
Authors: Chang, C. / Chhor, G. / Cobb, G. / Joachimiak, A.

History

Deposition	Nov 4, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kk4.cif.gz	124.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3kk4.ent.gz	99.1 KB	Display	PDB format
PDBx/mmJSON format	3kk4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kk4_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	3kk4_full_validation.pdf.gz	468.9 KB	Display
Data in XML	3kk4_validation.xml.gz	29 KB	Display
Data in CIF	3kk4_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kk/3kk4 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kk4	HTTPS FTP

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Related structure data

Similar structure data	2trx-4 2trx-3 1pu6-2 2fd3-d 4f7d-2 1ihn-d 3lrx-4 1zt9-1 2fch-12 2gwr-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 - HomologyF&H Search
Other databases	TargetDB: APC89551

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein BP1543

B: uncharacterized protein BP1543

C: uncharacterized protein BP1543

D: uncharacterized protein BP1543

hetero molecules

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

1

A: uncharacterized protein BP1543

B: uncharacterized protein BP1543

hetero molecules

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

2

C: uncharacterized protein BP1543

D: uncharacterized protein BP1543

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.212, 72.462, 61.737
Angle α, β, γ (deg.)	90.00, 112.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	uncharacterized protein BP1543 Mass: 14359.123 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Gene: Bordetella pertussis Tohama I, BP1543 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7VY20
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium Acetate, 0.1M This-Cl pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97962 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2009
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97962 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. all: 28802 / Num. obs: 28761 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 17.9 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 55.43
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.161 / Mean I/σ(I) obs: 16.76 / Num. unique all: 1402 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHENIX		model building
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→50 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.947 / SU B: 7.566 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19921	1457	5.1 %	RANDOM
R_work	0.14518	-	-	-
all	0.14792	28740	-	-
obs	0.14792	28740	99.58 %	-

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: 10.118 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0 Å²	0.66 Å²
2-	-	0.62 Å²	0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4000	0	10	440	4450

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4224
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.275	1.971	5734
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.648	5	528
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.376	22.273	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.368	15	719
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.725	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	638
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3299
X-RAY DIFFRACTION	r_gen_planes_other
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	0.584	1.5	2591
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.053	2	4176
X-RAY DIFFRACTION	r_scbond_it	1.744	3	1633
X-RAY DIFFRACTION	r_scangle_it	2.833	4.5	1558
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.948→1.999 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.222	98	-
R_work	0.15	1921	-
obs	-	2019	95.96 %

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	2.9545	-1.4588	-1.6942	3.6753	0.0488	1.6614	0.1018	0.3077	0.0791	-0.1191	0.022	0.0267	0.0536	-0.2264	-0.1238	0.039	-0.0106	-0.0232	0.0846	0.0219	0.028	11.9928	22.9727	-8.4723
2	8.9199	-1.3294	-0.9242	0.3532	-0.255	0.9273	-0.0854	0.2228	-0.7512	-0.067	-0.026	0.1021	0.0974	-0.0057	0.1114	0.0999	0.009	0.0059	0.0545	-0.0147	0.101	31.9205	11.9949	-8.2095
3	3.1522	0.558	-0.5198	2.4207	-0.9265	3.9219	0.028	0.0811	0.1324	-0.1919	-0.1787	-0.1258	0.0548	0.1349	0.1507	0.057	0.0297	0.0085	0.0564	0.0265	0.0269	34.57	24.8935	-8.8494
4	1.7153	-0.2904	0.4993	0.864	0.0194	3.2243	0.0182	-0.0557	-0.1161	-0.0211	-0.0849	-0.1176	0.103	0.232	0.0667	0.0395	0.0211	0.0035	0.0481	0.0232	0.0526	38.6275	15.8467	2.0251
5	4.4479	0.569	-0.053	8.1264	-0.7078	-0.6103	-0.0591	-0.1323	0.4554	0.1268	0.0607	0.1022	-0.0972	-0.0196	-0.0016	0.1345	0.0196	-0.0097	0.0886	-0.0126	0.0882	28.1707	30.7083	2.7848
6	5.2759	-0.5061	-1.9192	3.4853	-0.676	4.2947	0.1725	0.0841	0.4136	-0.1118	-0.1383	0.0054	-0.3785	0.3157	-0.0343	0.1298	-0.0463	-0.0201	0.0595	-0.0102	0.185	37.0596	34.9933	2.0916
7	4.3075	-1.7925	-1.8854	0.6687	0.4899	2.7682	-0.0706	-0.3486	0.2217	0.0682	0.1484	-0.0163	-0.1192	0.0974	-0.0778	0.0926	-0.0081	-0.0239	0.0709	-0.0248	0.0733	33.714	26.0167	13.6115
8	4.4335	2.2789	-1.7172	4.0391	-1.8213	1.948	0.0104	-0.2418	0.1142	0.0262	-0.0256	0.0433	0.2259	0.1121	0.0151	0.0723	0.0139	-0.0107	0.0757	-0.009	0.0375	35.4595	22.272	7.9139
9	7.4484	0.693	1.6424	0.1085	-0.0399	0.9913	0.2541	-0.312	-0.6392	0.0425	-0.0797	0.015	0.1068	-0.1375	-0.1744	0.1208	-0.0231	-0.0026	0.152	0.0041	0.1634	15.623	10.9254	6.2419
10	2.8415	-0.3129	-0.857	4.0595	-0.0604	2.2318	0.0925	-0.1411	0.1355	0.2517	-0.1201	0.0393	-0.1225	-0.0189	0.0276	0.0945	-0.0221	0.0199	0.0787	-0.0268	0.0181	13.1174	23.8719	8.9004
11	0.63	0.3931	0.8537	0.9225	-0.8139	2.9046	0.061	0.049	-0.0064	0.0355	0.0358	0.0959	0.0553	-0.1407	-0.0969	0.0499	-0.0047	0.0035	0.1075	-0.0034	0.0819	9.267	16.3296	-2.8153
12	3.1753	-0.6069	0.6967	8.5563	-2.0269	4.3491	0.1512	0.0181	0.4571	0.1275	-0.1263	-0.0027	-0.4021	0.1774	-0.0249	0.0784	-0.0099	0.0319	0.0732	0.008	0.0868	19.5762	30.9876	-2.2423
13	3.5399	-0.739	-3.8386	2.8477	-0.6822	8.0724	0.1009	-0.2108	0.69	0.1391	-0.0564	-0.0694	-0.3283	-0.0568	-0.0444	0.1633	0.0127	0.016	0.0865	-0.0414	0.3101	10.4698	35.5855	-0.7121
14	5.7967	2.2607	-1.4106	2.5301	-0.7415	1.4444	0.0539	0.3549	0.1463	-0.0667	0.0247	-0.126	-0.0955	-0.0554	-0.0786	0.0705	0.029	-0.0066	0.1121	0.0634	0.063	13.4954	27.5138	-13.4412
15	4.7372	-2.0848	-2.3556	5.0963	0.3121	3.3192	0.0505	0.1473	-0.1776	-0.1982	-0.0601	0.1028	0.1215	-0.1346	0.0096	0.0449	-0.0226	-0.0395	0.0396	-0.0066	0.0306	0.7458	41.6069	21.1943
16	5.5003	-3.1409	-1.393	1.5632	0.4942	0.1808	0.1087	0.0141	-0.3387	-0.0094	-0.0825	0.0916	-0.0309	-0.0082	-0.0262	0.185	0.0149	-0.0206	0.1263	-0.006	0.1659	20.8737	30.3902	21.306
17	3.0158	1.1461	-0.3631	2.7863	-0.3124	2.9295	0.0178	0.0666	-0.0339	-0.0943	-0.0703	-0.1215	0.0443	0.0774	0.0524	0.0523	0.021	0.0038	0.0618	0.025	0.0509	23.4018	43.6871	20.5774
18	2.0477	-0.1947	0.0051	1.0402	1.0097	2.4868	0.0249	0.0187	-0.1124	0.072	0.0998	-0.0935	0.1202	0.1096	-0.1246	0.0333	0.0152	-0.016	0.0247	-0.0052	0.0524	27.1552	34.6211	31.7499
19	3.4648	-0.0261	0.6915	2.5807	0.1592	2.0738	-0.0111	-0.1706	0.272	0.0242	-0.0207	-0.0602	-0.1924	-0.0706	0.0318	0.0413	-0.0032	-0.0111	0.0503	-0.0025	0.0577	17.1141	49.605	32.5232
20	3.6442	-0.1517	-2.6132	3.0138	0.3752	1.849	0.0887	0.0013	0.3764	0.0046	-0.169	-0.0679	-0.1817	0.3102	0.0803	0.1717	-0.0315	-0.0445	0.1588	0.0414	0.2294	26.1807	53.7501	31.7129
21	3.148	-0.0781	-1.526	-0.3723	-0.4212	2.6293	0.1572	-0.0221	0.1306	-0.0252	-0.0421	0.1026	-0.0093	-0.0249	-0.1151	0.1186	-0.0069	-0.0279	0.1271	-0.0827	0.1407	23.0562	44.7508	43.0155
22	5.5578	3.1545	-1.993	7.0821	-0.5999	0.7517	0.1038	-0.2442	-0.0246	0.2813	-0.0951	0.2208	0.1004	0.0417	-0.0087	0.0673	0.0154	-0.0458	0.0792	-0.0188	0.0439	24.4177	41.0594	37.342
23	8.8628	2.421	0.2649	0.9595	0.0072	0.5068	0.1031	-0.3219	-0.4913	-0.0237	-0.0671	-0.0038	0.048	-0.0354	-0.036	0.1287	0.0026	-0.0017	0.0867	0.0163	0.1366	4.2915	30.1164	36.3838
24	3.3094	-1.2935	-0.6931	3.301	0.2958	2.6733	0.0079	-0.0789	0.0665	0.2577	-0.0182	-0.0496	-0.0614	0.0683	0.0102	0.0662	-0.0272	0.0085	0.0692	-0.0074	0.0029	2.1237	43.193	38.3352
25	1.7292	0.0008	0.8341	1.4647	-1.5393	3.3984	0.0939	-0.0153	-0.1625	-0.1015	0.0181	0.1199	0.2367	-0.1623	-0.112	0.0412	-0.0141	-0.0066	0.0226	-0.0058	0.0626	-2.0604	35.3114	26.9158
26	2.7961	-1.3901	0.446	4.5687	0.2183	2.472	0.0366	0.0517	0.3285	-0.0252	-0.0162	-0.1638	-0.2811	0.0961	-0.0205	0.045	-0.0161	0.0128	0.0467	0.0045	0.0416	8.3771	50.1875	27.084
27	3.3997	-0.755	-1.2296	4.1538	-0.2591	4.1684	0.0626	-0.0341	0.1898	-0.0704	-0.1417	0.0714	-0.165	-0.2102	0.0791	0.1026	0.0175	0.0227	0.0348	-0.0116	0.1055	-0.8013	54.6256	28.472
28	5.6909	1.3772	-4.0008	4.0288	-1.139	1.5378	0.1039	0.3801	0.225	-0.1317	0.0392	0.0101	-0.0433	-0.2019	-0.143	0.1089	0.0145	-0.0283	0.0942	0.0177	0.0223	2.3499	46.3922	15.9193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 34
3	X-RAY DIFFRACTION	3	A	35 - 50
4	X-RAY DIFFRACTION	4	A	51 - 78
5	X-RAY DIFFRACTION	5	A	79 - 90
6	X-RAY DIFFRACTION	6	A	91 - 109
7	X-RAY DIFFRACTION	7	A	110 - 121
8	X-RAY DIFFRACTION	8	B	1 - 12
9	X-RAY DIFFRACTION	9	B	13 - 34
10	X-RAY DIFFRACTION	10	B	35 - 50
11	X-RAY DIFFRACTION	11	B	51 - 78
12	X-RAY DIFFRACTION	12	B	79 - 90
13	X-RAY DIFFRACTION	13	B	91 - 109
14	X-RAY DIFFRACTION	14	B	110 - 121
15	X-RAY DIFFRACTION	15	C	1 - 12
16	X-RAY DIFFRACTION	16	C	13 - 34
17	X-RAY DIFFRACTION	17	C	35 - 50
18	X-RAY DIFFRACTION	18	C	51 - 78
19	X-RAY DIFFRACTION	19	C	79 - 90
20	X-RAY DIFFRACTION	20	C	91 - 109
21	X-RAY DIFFRACTION	21	C	110 - 121
22	X-RAY DIFFRACTION	22	D	1 - 12
23	X-RAY DIFFRACTION	23	D	13 - 34
24	X-RAY DIFFRACTION	24	D	35 - 50
25	X-RAY DIFFRACTION	25	D	51 - 78
26	X-RAY DIFFRACTION	26	D	79 - 90
27	X-RAY DIFFRACTION	27	D	91 - 109
28	X-RAY DIFFRACTION	28	D	110 - 121

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Yorodumi