PDB-4mh4: Crystal Structure of OsmC-like protein from Burkholderia cenocepa...

ID or keywords:

Entry

Database: PDB / ID: 4mh4

Title

Crystal Structure of OsmC-like protein from Burkholderia cenocepacia J2315

Components

OsmC-like protein

Keywords

PROTEIN BINDING /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OsmC-like protein /

peroxiredoxin

Function / homology

Function and homology information

response to oxidative stress
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal Structure of OsmC-like protein from Burkholderia cenocepacia J2315
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.

History

Deposition	Aug 29, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 16, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mh4.cif.gz	119.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4mh4.ent.gz	93.3 KB	Display	PDB format
PDBx/mmJSON format	4mh4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mh/4mh4 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mh4	HTTPS FTP

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Related structure data

Related structure data	1zb8S S: Starting model for refinement
Similar structure data	3llk-3 6ebc-2 1tab-d 3n35-d 3aja-2 6ebg-2 6eci-3 1zb9-d 6mjn-2 3aja-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BuceA.00074.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: OsmC-like protein

B: OsmC-like protein

31 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.940, 87.940, 44.940
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	OsmC-like protein Mass: 15523.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: BceJ2315_17290, BCAL1766 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E9U7
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.05 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: JCSG+(c1): 20%PEG-8000, 100mM Sodium Phosphate Dibasic/ Citric Acid 200mM Sodium Chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.9786 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2013 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. all: 27401 / Num. obs: 27321 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 35.005 Å² / R_merge(I) obs: 0.037 / Net I/σ(I): 30.53

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.9-1.95		0.419	4.32	11861	2016	100
1.95-2		0.316	5.76	11478	1953	99.7
2-2.06		0.245	7.39	11291	1921	99.9
2.06-2.12		0.175	10.04	10548	1818	100
2.12-2.19		0.142	12.37	10448	1806	99.9
2.19-2.27		0.114	15.25	9977	1734	100
2.27-2.36		0.091	18.29	9723	1690	100
2.36-2.45		0.084	19.93	9174	1594	99.9
2.45-2.56		0.064	24.83	8804	1544	100
2.56-2.69		0.049	31.68	8589	1510	100
2.69-2.83		0.041	37.15	7948	1411	100
2.83-3		0.033	44.49	7562	1338	99.9
3-3.21		0.028	51.69	7010	1263	99.8
3.21-3.47		0.024	60.09	6535	1171	99.7
3.47-3.8		0.022	68.06	5940	1079	99.6
3.8-4.25		0.021	73.26	5417	974	99.6
4.25-4.91		0.02	77.5	4836	874	99.4
4.91-6.01		0.02	75.6	4066	729	98.2
6.01-8.5		0.018	76.85	3118	577	98.5
	8.5	0.018	76.65	1502	319	92.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.9 Å	43.97 Å
Translation	3.46 Å	43.97 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZB8

1zb8

Resolution: 1.9→19.75 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.1922 / WR_factor R_work: 0.1621 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8839 / SU B: 4.894 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1155 / SU R_free: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1961	1372	5 %	RANDOM
R_work	0.1655	-	-	-
all	0.167	28664	-	-
obs	0.167	27292	99.68 %	-

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 max: 60.43 Å² / B_iso mean: 32.948 Å² / B_iso min: 7.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-0 Å²	-0 Å²
2-	-	-0.12 Å²	-0 Å²
3-	-	-	0.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1962	0	0	222	2184

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	2029
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1904
X-RAY DIFFRACTION	r_angle_refined_deg	1.493	1.957	2774
X-RAY DIFFRACTION	r_angle_other_deg	0.735	3	4357
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.047	5	285
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.449	23.976	83
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.582	15	296
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.506	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	327
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2419
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	453
X-RAY DIFFRACTION	r_mcbond_it	0.96	1.498	1110
X-RAY DIFFRACTION	r_mcbond_other	0.959	1.498	1109
X-RAY DIFFRACTION	r_mcangle_it	1.483	2.24	1387

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.258	103	-
R_work	0.22	1886	-
all	-	1989	-
obs	-	-	99.95 %

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	9.6701	-3.9431	5.8328	5.8612	-1.7572	5.109	0.0396	-0.4467	0.1173	0.5385	0.1737	-0.4771	-0.0488	0.0257	-0.2133	0.1948	-0.0597	-0.0451	0.1242	0.0134	0.1681	16.0097	33.207	21.4447
2	20.1315	4.7204	18.2337	5.688	10.644	25.3796	0.5181	-1.6604	-0.0316	-0.0056	-0.9662	0.2962	0.3251	-2.3064	0.4481	0.2923	-0.0574	0.0196	0.3169	0.0531	0.3301	-6.3377	37.24	13.913
3	6.7692	4.5784	-0.5481	4.8784	1.4595	4.7141	-0.1121	-0.0751	0.1879	-0.1601	0.0912	0.06	0.0866	0.0723	0.0209	0.2171	-0.0141	-0.0234	0.0421	0.0544	0.1645	3.0044	38.3221	8.2105
4	5.9761	-1.3457	1.07	1.6859	-0.3021	0.7868	-0.1486	0.1147	0.1933	-0.1012	0.0766	-0.0756	-0.0863	0.1493	0.072	0.1789	-0.0189	0.0577	0.0781	0.0073	0.1199	4.9243	23.7638	8.4332
5	20.3061	-5.1777	18.4385	5.3876	-2.3833	22.6278	0.0025	0.6111	0.5517	-0.2885	0.1263	-0.5095	-0.6427	0.94	-0.1288	0.1311	-0.0315	0.1534	0.3246	0.0155	0.3215	27.6589	17.6078	4.5937
6	10.6801	2.3155	-8.755	1.8359	-1.5921	9.7551	0.0597	0.1394	-0.2764	-0.2304	-0.1936	-0.1314	0.0163	0.0966	0.1339	0.1995	0.0134	0.023	0.0884	0.0205	0.1069	4.2958	16.504	7.0405
7	10.4861	-1.9734	-10.476	4.377	3.982	15.9616	0.2125	0.2656	0.0955	0.0751	-0.2126	0.2394	-0.0031	-0.5498	0	0.1524	-0.0146	-0.0054	0.0853	0.0278	0.0941	-3.388	15.3571	16.6732
8	25.9022	-9.7594	-15.0736	3.6814	5.5912	12.1415	0.5087	0.5023	0.1966	-0.2239	-0.1854	-0.0843	0.133	0.0594	-0.3233	0.3765	-0.0009	0.1377	0.267	-0.0885	0.1881	16.4848	11.9433	0.7281
9	5.7419	-8.1222	-1.4324	11.4946	2.2235	41.2502	0.425	-0.1433	-0.4444	-0.5131	0.2598	0.6395	1.4178	0.1584	-0.6847	0.2738	0.0767	-0.0008	0.3524	-0.1583	0.3652	22.1548	6.089	4.9018
10	1.3452	-1.0385	-0.2683	1.1285	0.8622	1.5046	0.0516	0.0272	0.0568	-0.0717	0.0403	-0.1632	-0.0762	0.1728	-0.0919	0.1374	-0.0037	0.0308	0.1435	0.0048	0.2426	14.9473	15.1295	16.5362
11	20.892	-6.4498	-22.6108	6.6834	9.7378	27.98	-0.266	0.1049	-0.1123	-0.0118	0.1345	-0.1526	0.4673	-0.0258	0.1316	0.182	0.0432	0.0035	0.0847	-0.0047	0.1293	9.2677	9.3601	10.0692
12	14.2626	-1.3093	1.22	4.6582	-3.5558	16.7829	-0.1004	-0.2719	-0.259	0.3934	0.0186	-0.0703	0.1565	-0.0809	0.0819	0.1339	-0.0694	0.0038	0.0638	-0.0146	0.0904	-8.7079	11.44	15.8171
13	11.0126	3.7043	-4.325	2.6048	-1.381	3.8394	-0.04	0.0103	-0.1319	-0.3492	-0.0232	-0.2303	0.0054	0.3237	0.0632	0.2193	-0.0019	0.0647	0.1217	0.0328	0.128	7.4115	22.0856	3.1034
14	14.5381	2.9598	0.2405	3.6668	0.9792	1.4078	-0.1728	0.1519	0.4096	-0.2759	0.1299	-0.1443	-0.0338	0.2734	0.0429	0.1916	-0.014	0.0589	0.0832	0.0542	0.105	7.1891	28.3126	1.8176
15	5.2945	-1.1952	-0.8427	4.7091	2.7817	8.2505	-0.0122	0.1845	0.2454	0.0003	0.1684	-0.2207	-0.2751	0.5239	-0.1562	0.1489	-0.0404	0.0402	0.0729	0.0118	0.1459	11.6759	32.4694	9.8484
16	5.7056	1.0158	-2.964	3.1049	-0.3792	2.668	-0.37	0.0823	0.0613	-0.1089	0.1236	0.1528	0.2414	-0.116	0.2464	0.2073	-0.0158	0.0492	0.0273	0.013	0.1568	-5.6788	30.3226	20.0447
17	15.0016	10.9805	-7.5699	22.2285	-8.4833	7.8437	-0.1831	0.0958	0.4665	-0.4224	0.0694	1.059	-0.2184	-0.4164	0.1137	0.1134	0.0176	-0.0128	0.0554	-0.0527	0.222	-15.7005	36.2826	23.2484
18	5.6964	-3.1699	0.8504	5.2453	-0.4848	1.1946	-0.0915	0.0805	0.21	0.3205	0.0101	-0.4404	-0.184	0.187	0.0814	0.1791	-0.0346	-0.0048	0.077	-0.0053	0.1348	11.9569	31.0521	21.5609
19	34.5774	-20.8914	0.0083	15.2276	0.8789	5.3391	-0.0756	-0.3628	0.0077	-0.0593	-0.0422	0.287	-0.1994	-0.2585	0.1178	0.2139	-0.0229	0.026	0.0638	-0.0129	0.1502	-3.159	39.509	24.6768
20	1.3428	4.9112	-2.9362	28.6152	-5.536	8.9703	0.1774	0.0732	0.1817	1.0721	0.0019	1.1643	-0.2531	-0.3048	-0.1792	0.2563	-0.0366	0.0876	0.2402	-0.0612	0.2183	-11.0803	37.8685	32.9635
21	6.8096	-2.3378	-1.5555	1.8103	0.0242	0.72	-0.0623	-0.2444	0.1206	0.1555	0.0856	-0.1351	-0.113	0.076	-0.0234	0.1854	-0.0113	0.0332	0.0451	-0.0094	0.1337	-1.5774	24.7007	25.895
22	30.1919	-32.3025	-2.6756	38.0208	4.0183	0.6277	-0.366	-0.5046	0.7026	0.3009	0.4672	-0.8163	-0.0074	0.0492	-0.1012	0.26	-0.0218	0.0364	0.2037	-0.0298	0.1256	3.129	34.6713	29.1368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 21
2	X-RAY DIFFRACTION	2	A	22 - 28
3	X-RAY DIFFRACTION	3	A	29 - 42
4	X-RAY DIFFRACTION	4	A	43 - 75
5	X-RAY DIFFRACTION	5	A	76 - 83
6	X-RAY DIFFRACTION	6	A	84 - 97
7	X-RAY DIFFRACTION	7	A	98 - 107
8	X-RAY DIFFRACTION	8	A	108 - 114
9	X-RAY DIFFRACTION	9	A	115 - 120
10	X-RAY DIFFRACTION	10	A	121 - 140
11	X-RAY DIFFRACTION	11	A	141 - 147
12	X-RAY DIFFRACTION	12	B	11 - 16
13	X-RAY DIFFRACTION	13	B	17 - 28
14	X-RAY DIFFRACTION	14	B	29 - 47
15	X-RAY DIFFRACTION	15	B	48 - 59
16	X-RAY DIFFRACTION	16	B	60 - 75
17	X-RAY DIFFRACTION	17	B	76 - 85
18	X-RAY DIFFRACTION	18	B	86 - 106
19	X-RAY DIFFRACTION	19	B	107 - 112
20	X-RAY DIFFRACTION	20	B	113 - 121
21	X-RAY DIFFRACTION	21	B	122 - 140
22	X-RAY DIFFRACTION	22	B	141 - 147

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