PDB-6p1e: Cu-bound PmoF1 PCuAC domain (dimer)

ID or keywords:

Entry

Database: PDB / ID: 6p1e

Title

Cu-bound PmoF1 PCuAC domain (dimer)

Components

PmoF1

Keywords

METAL BINDING PROTEIN /

copper binding protein /

chaperone

Function / homology

COPPER (II) ION / THIOCYANATE ION

Function and homology information

Biological species

Methylocystis sp. ATCC 49242 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.605 Å

Authors

Fisher, O.S. / Sendzik, M.R. / Rosenzweig, A.C.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	F32GM119191	United States
Department of Energy (DOE, United States)	DE-SC0016284	United States

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: PCuAC domains from methane-oxidizing bacteria use a histidine brace to bind copper.
Authors: Fisher, O.S. / Sendzik, M.R. / Ross, M.O. / Lawton, T.J. / Hoffman, B.M. / Rosenzweig, A.C.

History

Deposition	May 19, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 13, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6p1e.cif.gz	116.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6p1e.ent.gz	89.4 KB	Display	PDB format
PDBx/mmJSON format	6p1e.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/p1/6p1e ftp://data.pdbj.org/pub/pdb/validation_reports/p1/6p1e	HTTPS FTP

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Related structure data

Related structure data	6p16C 6p17C 6p1fC 6p1gC C: citing same article (ref.)
Similar structure data	6p16-d 1hw4-d 5ioh-1 3w2h-d 3eaw-d 5e9q-1 3bzj-d 5gv8-d 1umk-d 3w2i-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: PmoF1

B: PmoF1

hetero molecules

26.8 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)	55.407, 60.486, 76.836
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PmoF1 Mass: 13258.194 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylocystis sp. ATCC 49242 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.43 Å³/Da / Density % sol: 49.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate, 20% PEG3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.37 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.37 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 33794 / % possible obs: 98 % / Redundancy: 10 % / R_merge(I) obs: 0.07 / R_pim(I) all: 0.021 / R_rim(I) all: 0.073 / Χ²: 0.987 / Net I/σ(I): 16.3 / Num. measured all: 336434

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.6-1.66	5.1	0.392	2935	0.942	0.174	0.43	0.707	87.2
1.66-1.72	6.7	0.402	3338	0.778	0.155	0.433	1.038	97.8
1.72-1.8	9	0.351	3358	0.986	0.118	0.371	0.786	99.6
1.8-1.9	10.1	0.243	3388	0.988	0.078	0.256	0.764	99.2
1.9-2.02	9.3	0.137	3379	0.994	0.046	0.145	0.946	99.1
2.02-2.17	11.7	0.098	3415	0.996	0.029	0.103	0.938	99.8
2.17-2.39	11.5	0.078	3428	0.996	0.023	0.081	1.114	99.8
2.39-2.74	12.2	0.066	3473	0.997	0.019	0.068	1.017	99.9
2.74-3.45	10.8	0.055	3444	0.996	0.018	0.058	1.232	98.8
3.45-50	12.2	0.063	3636	0.991	0.019	0.066	1.074	98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.8.3_1479	refinement
HKL-2000		data reduction
HKL-2000		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.605→44.941 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.68

	R_factor	Num. reflection	% reflection
R_free	0.1905	2808	4.78 %
R_work	0.1727	-	-
obs	0.1735	32891	90.03 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 135.45 Å² / B_iso mean: 26.82 Å² / B_iso min: 3.76 Å²

Refinement step

Cycle: final / Resolution: 1.605→44.941 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1835	0	8	317	2160
B_iso mean	-	-	30.57	34.13	-
Num. residues	-	-	-	-	241

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1898
X-RAY DIFFRACTION	f_angle_d	1.014	2579
X-RAY DIFFRACTION	f_chiral_restr	0.039	290
X-RAY DIFFRACTION	f_plane_restr	0.004	332
X-RAY DIFFRACTION	f_dihedral_angle_d	11.74	685

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6049-1.6326	0.2781	68	0.2532	1546	1614	50
1.6326-1.6623	0.2659	96	0.2352	1776	1872	58
1.6623-1.6943	0.225	112	0.2157	2113	2225	69
1.6943-1.7289	0.2523	131	0.2008	2408	2539	77
1.7289-1.7665	0.2161	133	0.1987	2535	2668	83
1.7665-1.8075	0.2547	133	0.1967	2764	2897	88
1.8075-1.8527	0.2578	128	0.1956	2863	2991	92
1.8527-1.9028	0.1874	179	0.1941	2915	3094	95
1.9028-1.9588	0.2336	145	0.178	3021	3166	97
1.9588-2.0221	0.1905	116	0.1806	3075	3191	98
2.0221-2.0943	0.1826	153	0.1704	3099	3252	100
2.0943-2.1782	0.1684	140	0.1683	3118	3258	100
2.1782-2.2773	0.2049	158	0.1644	3079	3237	100
2.2773-2.3974	0.1882	180	0.1686	3077	3257	100
2.3974-2.5476	0.2073	151	0.1742	3122	3273	100
2.5476-2.7442	0.2263	143	0.177	3136	3279	100
2.7442-3.0203	0.2227	167	0.1802	3063	3230	100
3.0203-3.4573	0.1705	152	0.1669	3046	3198	98
3.4573-4.3552	0.155	157	0.1501	3053	3210	98
4.3552-44.9587	0.1469	166	0.1551	3076	3242	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	5.5402	-1.2383	2.8716	4.4167	-0.1042	5.27	-0.0764	-0.1822	-0.2591	0.0636	0.2153	0.0167	0.2251	-0.1586	-0.0438	0.0475	-0.0053	0.0362	0.026	-0.0318	0.0803	50.9127	0.7146	18.839
2	4.5674	3.4465	-3.0965	5.8338	-6.218	8.0286	0.1184	1.1362	1.2874	-0.6143	0.0282	0.2027	-0.7225	-0.3428	-0.2242	1.0133	-0.0104	-0.1038	0.4813	0.2693	0.5642	47.0213	17.9101	3.4547
3	2.161	0.2608	0.3841	3.3506	-0.6531	3.1949	-0.0647	0.0756	0.0688	-0.1992	0.0038	-0.2103	-0.0016	0.237	0.0227	0.0812	-0.0042	0.0361	0.0502	-0.0071	0.0701	56.1053	9.1407	19.0127
4	0.9946	-0.1849	0.0236	3.1695	-0.6135	0.6058	0.1298	-0.134	0.0737	0.7338	-0.0207	0.3231	-0.1007	-0.1186	0.1007	0.2155	-0.0314	0.0841	-0.0017	0.0457	0.1791	53.6023	20.9581	24.0992
5	2.0321	-0.4336	2.1725	3.3399	-1.2414	3.1749	-0.0874	-0.2055	0.1663	0.1139	0.0445	0.1619	-0.048	-0.1035	-0.0357	0.0963	0.0002	0.0267	0.0531	-0.014	0.095	51.4362	11.1488	23.7831
6	3.3039	1.6468	-1.2258	3.759	-0.7287	0.4598	-0.32	1.2407	0.0866	-0.828	0.2201	0.1903	-0.4424	-0.1466	0.0287	0.6267	-0.1795	-0.0161	0.5567	-0.0117	0.1659	50.9071	8.3033	0.5349
7	4.7881	-1.7074	4.5403	3.4437	-1.7077	7.6647	0.0407	0.2159	-0.1413	-0.281	0.0346	-0.2633	0.1494	0.3117	-0.0975	0.1052	-0.0082	0.059	0.0522	-0.002	0.1089	57.1723	4.4871	14.7922
8	3.791	0.1259	4.2968	0.5085	-0.1514	5.0436	-0.1317	-0.0275	-0.5156	-0.0339	0.1297	-0.6729	0.0395	0.4832	-0.1751	0.1572	-0.0635	-0.0706	0.2446	0.0665	0.3114	39.4745	-7.3066	20.8995
9	7.5139	2.9114	2.2475	4.5674	0.6563	4.2357	0.0314	-0.1271	-0.0777	0.0256	0.1182	-0.1316	0.1458	-0.0567	-0.121	0.0057	-0.0095	0.0044	0.0911	0.0123	0.061	37.8817	-0.3601	19.6139
10	8.676	-5.7451	-6.0395	7.3038	3.0706	4.4512	-0.1929	-0.7969	0.9552	0.349	0.223	-0.3303	-0.2321	0.1816	-0.3537	0.4568	0.1243	0.0521	0.7475	-0.3182	0.4232	32.9536	15.2971	34.3257
11	2.038	-0.156	0.1196	2.6649	1.1928	2.2531	0.0479	-0.0091	-0.0224	-0.1981	-0.0455	0.3209	-0.0366	-0.5307	-0.0304	0.0887	-0.0145	-0.0272	0.2218	-0.0086	0.1129	31.2754	-0.4022	14.9321
12	4.0584	-0.7362	1.1007	1.7568	1.1945	3.4448	-0.0117	-0.8144	-0.1569	0.5098	0.0429	0.4156	0.1802	-0.5875	0.0673	0.1806	0.0445	0.0923	0.456	0.0066	0.1855	26.0882	4.9849	28.4983
13	8.393	-3.7532	-5.1031	9.1567	7.869	7.2777	0.5905	0.6109	0.5365	-1.1023	-0.0301	0.031	-0.7977	-0.3228	-0.5353	0.2332	0.1227	-0.0043	0.2922	0.0159	0.335	25.5185	12.7857	14.2778
14	6.57	-3.8471	-4.3131	7.9242	5.0915	3.9934	0.1483	0.4779	0.0412	-0.743	-0.034	0.2289	-0.1692	-0.4364	0.0325	0.189	-0.0014	-0.056	0.2391	-0.0075	0.1098	30.6254	0.0247	7.4306
15	4.0629	-0.2514	-0.5677	5.136	-0.0648	1.2151	-0.0516	-0.0267	0.3831	-0.2603	0.0828	0.0946	-0.1783	-0.2767	-0.0141	0.0679	0.0196	-0.0158	0.1791	0.0007	0.1076	33.3784	7.8634	17.7031
16	4.4192	-2.4225	-1.2793	6.242	-2.1189	1.9885	0.0259	-0.9753	0.3156	1.1642	-0.4188	-0.3119	-0.5106	0.1815	0.3323	0.6391	-0.1226	0.0727	0.8416	-0.0229	0.3082	34.7183	6.0009	37.973
17	7.2015	3.0437	5.5467	3.4602	3.1309	5.5038	0.2656	-0.4525	-0.1825	0.1754	-0.104	0.3984	0.1244	-0.5469	0.2956	0.1011	-0.0568	0.0239	0.3702	0.0254	0.2127	28.1822	-3.668	21.8929
18	3.8799	4.4681	4.0321	7.3898	3.2904	7.2912	0.1031	-0.9195	0.2253	0.3646	-0.2339	0.2192	0.0519	-0.4514	0.0082	0.0859	0.0158	0.0235	0.2957	-0.0412	0.1861	35.7653	-0.1047	27.2811

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 48 )	A	32 - 48
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 56 )	A	49 - 56
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 87 )	A	57 - 87
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 98 )	A	88 - 98
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 99 through 119 )	A	99 - 119
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 130 )	A	120 - 130
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 131 through 151 )	A	131 - 151
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 32 through 37 )	B	32 - 37
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 38 through 48 )	B	38 - 48
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 56 )	B	49 - 56
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 57 through 77 )	B	57 - 77
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 78 through 87 )	B	78 - 87
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 88 through 98 )	B	88 - 98
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 99 through 104 )	B	99 - 104
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 105 through 119 )	B	105 - 119
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 120 through 129 )	B	120 - 129
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 130 through 140 )	B	130 - 140
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 141 through 152 )	B	141 - 152

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