PDB-6mjs: Azurin 122W/124W/126Re

ID or keywords:

Entry

Database: PDB / ID: 6mjs

Title

Azurin 122W/124W/126Re

Components

Azurin

Keywords

ELECTRON TRANSPORT / Electron Hopping

Function / homology

Function and homology information

transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Takematsu, K. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R. / Williamson, H. / Kaiser, J.T. / Heyda, J. / Hollas, D.

Funding support

United States, 1items

Citation

Journal: ACS Cent Sci / Year: 2019
Title: Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein.
Authors: Takematsu, K. / Williamson, H.R. / Nikolovski, P. / Kaiser, J.T. / Sheng, Y. / Pospisil, P. / Towrie, M. / Heyda, J. / Hollas, D. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R.

History

Deposition	Sep 21, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mjs.cif.gz	289.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6mjs.ent.gz	239.5 KB	Display	PDB format
PDBx/mmJSON format	6mjs.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6mjs_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	6mjs_full_validation.pdf.gz	3.5 MB	Display
Data in XML	6mjs_validation.xml.gz	24.2 KB	Display
Data in CIF	6mjs_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mj/6mjs ftp://data.pdbj.org/pub/pdb/validation_reports/mj/6mjs	HTTPS FTP

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Related structure data

Related structure data	6mjrC 6mjtC 4azuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mjt-2 4mfh-3 4ko7-4 5i28-14 5i28-6 3jtb-4 5i26-4 3n2j-7 5i28-15 5i28-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6mjrC

6mjtC

4azuS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Azurin

B: Azurin

C: Azurin

D: Azurin

hetero molecules

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

1

A: Azurin

hetero molecules

defined by author&software
14.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Azurin

hetero molecules

defined by author&software
14.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Azurin

hetero molecules

defined by author&software
14.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Azurin

hetero molecules

defined by author&software
14.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.072, 221.563, 89.996
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-347- HOH
2	1	B-363- HOH
3	1	B-364- HOH
4	1	C-371- HOH

#1: Protein	Azurin Mass: 14059.922 Da / Num. of mol.: 4 / Mutation: W48F, Y72F, H83Q, Y108F, K122W, T124W, T126H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-REQ / (1,10 PHENANTHROLINE)-(TRI-CARBON MONOXIDE) RHENIUM (I) Mass: 478.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₁₂N₂O₃Re / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 271 / 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	Density Matthews: 2.35 Å³/Da / Density % sol: 47.71 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / pH: 7.2 Details: 100 mM imidiazole, 100 mM LiNO3, 6.25 mM CuCl2, 28% PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2011 / Details: liquid nitrogen-cooled K-B focusing mirrors

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.85→34.926 Å / Num. all: 44003 / Num. obs: 44003 / % possible obs: 96.2 % / Redundancy: 3.3 % / R_pim(I) all: 0.048 / R_rim(I) all: 0.089 / R_sym value: 0.075 / Net I/av σ(I): 6.6 / Net I/σ(I): 8.3 / Num. measured all: 145966

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.85-1.95	3.4	0.848	0.9	21813	6369	0.534	1.006	0.848	1.4	96.3
1.95-2.07	3.3	0.496	1.5	20050	6060	0.321	0.593	0.496	2.5	96.9
2.07-2.21	3.4	0.282	2.5	19101	5613	0.179	0.335	0.282	4.1	95.2
2.21-2.39	3.4	0.198	3.5	18383	5348	0.126	0.236	0.198	5.6	98
2.39-2.62	3.3	0.139	5.2	15820	4831	0.09	0.166	0.139	7.4	95.7
2.62-2.93	3.3	0.095	7.3	15104	4525	0.062	0.114	0.095	10.4	97.7
2.93-3.38	3.2	0.065	10.2	12135	3807	0.043	0.078	0.065	14.3	93.6
3.38-4.14	3.3	0.05	12.7	11015	3378	0.032	0.06	0.05	19.4	97.2
4.14-5.85	3.1	0.046	13.4	8051	2586	0.03	0.056	0.046	21	94.4
5.85-34.926	3	0.041	13.8	4494	1486	0.026	0.049	0.041	20	93.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
SCALA	3.3.20	data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu

Resolution: 1.85→34.926 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.37

	R_factor	Num. reflection	% reflection
R_free	0.1978	2203	5.01 %
R_work	0.1687	-	-
obs	0.1702	43951	95.83 %

Solvent computation

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

Displacement parameters

B_iso max: 87.92 Å² / B_iso mean: 33.13 Å² / B_iso min: 14.83 Å²

Refinement step

Cycle: final / Resolution: 1.85→34.926 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3805	0	96	271	4172
B_iso mean	-	-	28.94	42.13	-
Num. residues	-	-	-	-	505

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3991
X-RAY DIFFRACTION	f_angle_d	1.416	5428
X-RAY DIFFRACTION	f_chiral_restr	0.078	588
X-RAY DIFFRACTION	f_plane_restr	0.006	691
X-RAY DIFFRACTION	f_dihedral_angle_d	12.542	1376

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.85-1.8902	0.3515	134	0.3192	2578	2712	95
1.8902-1.9342	0.3413	145	0.3012	2588	2733	97
1.9342-1.9826	0.293	133	0.2614	2591	2724	97
1.9826-2.0362	0.2951	156	0.2446	2565	2721	96
2.0362-2.0961	0.2558	138	0.2187	2551	2689	95
2.0961-2.1637	0.2268	141	0.1965	2558	2699	96
2.1637-2.241	0.2152	118	0.1808	2654	2772	97
2.241-2.3307	0.2515	119	0.1777	2635	2754	97
2.3307-2.4368	0.2244	125	0.1803	2668	2793	97
2.4368-2.5652	0.2318	149	0.1801	2493	2642	93
2.5652-2.7259	0.1999	138	0.1659	2668	2806	98
2.7259-2.9363	0.1922	144	0.174	2639	2783	97
2.9363-3.2316	0.19	128	0.1568	2621	2749	96
3.2316-3.6987	0.1615	151	0.1461	2546	2697	93
3.6987-4.6583	0.1627	123	0.1356	2703	2826	96
4.6583-34.9319	0.1693	161	0.1561	2690	2851	93

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	4.5556	-4.5441	-0.0126	4.7031	1.0653	7.6392	0.6417	1.0265	0.3683	-0.9426	-0.9929	-1.0109	-0.2647	1.0788	0.1337	0.296	-0.0036	-0.0296	0.5703	0.1371	0.5125	35.0471	-34.3636	4.5466
2	5.8439	-1.8589	-3.17	2.2341	1.1646	4.7429	0.145	0.3152	0.527	-0.5244	-0.2114	-0.5496	-0.5266	0.1633	-0.0341	0.3615	0.0056	-0.0128	0.2608	0.0516	0.3439	22.5842	-27.3382	4.3826
3	8.328	-2.4634	1.1834	0.9136	0.6783	5.7025	-0.1529	0.1013	0.1622	-0.0506	-0.152	-2.0963	0.766	1.2669	0.1089	0.3319	0.154	0.0014	0.3728	0.0767	0.6584	35.8905	-43.3319	-0.9898
4	2.7498	-0.4947	-0.9093	1.7127	0.8782	3.1539	-0.1107	-0.2168	0.1809	0.4789	0.1627	-0.6394	0.1236	0.6565	0.0035	0.2218	-0.0086	-0.1356	0.3419	0.0655	0.2622	29.329	-31.2223	11.0652
5	2.0949	-0.8643	-0.3903	7.0444	3.8714	4.3076	0.0207	-0.2547	-0.1847	0.476	-0.1151	-0.1031	0.5624	0.0137	0.0788	0.2249	0.024	-0.0383	0.2022	0.0653	0.1859	20.0786	-36.9071	10.1969
6	4.5608	-2.1601	-1.2208	3.8561	0.7734	4.3276	0.0124	-0.2665	-0.5424	0.5523	-0.0787	0.1683	0.4587	-0.0449	0.0944	0.3694	-0.0718	-0.0574	0.2306	0.0824	0.322	17.1497	-42.5244	14.1931
7	4.7256	-3.4961	-3.4038	4.5666	3.7482	4.8406	-0.5005	-0.5528	-0.2074	1.4122	0.4157	-0.4776	0.9042	0.6109	0.0259	0.3278	0.031	-0.1219	0.2775	0.0433	0.3348	30.1869	-38.3815	12.3281
8	8.7221	-4.8677	-3.9027	5.9312	1.3113	2.3026	-0.5195	-0.672	0.2557	0.3596	1.0865	-1.3355	1.807	1.4883	-0.4511	0.6308	0.1463	-0.0425	0.5295	-0.1953	0.4662	27.5394	-49.985	-3.6658
9	7.7552	-5.726	-4.2577	7.5312	3.9549	5.9031	0.0876	0.352	-0.4231	0.0051	-0.2534	0.1783	0.2077	-0.1585	0.1232	0.1538	0.0001	-0.0452	0.1333	0.0176	0.1708	20.6797	-37.663	3.0273
10	2.3666	-2.6089	0.2853	8.2499	-1.9618	2.5646	0.0625	-0.0943	-0.3344	-0.1587	0.0031	0.8985	0.3228	-0.3467	-0.0801	0.2407	-0.0742	0.0067	0.2517	-0.0423	0.3675	-5.206	-18.5814	3.5063
11	3.6203	-0.7225	0.1787	6.0001	0.051	2.3693	-0.1054	-0.1077	-0.0559	0.3917	0.0512	-0.1235	0.2327	0.0549	0.0703	0.2115	0.0413	0.052	0.1682	-0.0175	0.135	6.659	-20.1822	10.5226
12	3.9983	-2.345	1.2207	5.9832	-1.1838	2.0622	-0.1912	-0.4283	0.2222	0.5509	0.1823	0.2257	-0.212	-0.2133	0.036	0.2837	0.0057	0.0519	0.2431	-0.0371	0.2454	1.8134	-12.8171	11.7299
13	7.1795	-5.5111	2.984	4.3071	-2.7201	3.0523	-0.0247	0.1166	0.1903	-0.0009	-0.1956	-0.1826	0.1256	0.006	0.161	0.1782	-0.0268	0.0289	0.1738	-0.0237	0.19	5.1544	-17.7193	2.7851
14	5.1805	-0.6728	3.0244	2.782	-1.0128	6.7317	0.1349	-0.0664	-1.4232	-0.3288	0.1369	0.1498	0.5751	-0.6705	-0.2445	0.2826	-0.0517	0.0137	0.3176	0.0172	0.5292	11.5944	-23.0536	-18.9238
15	4.3678	0.0678	-0.1087	2.1193	0.4415	1.9056	-0.0612	0.1875	-0.5201	-0.1063	0.0402	-0.0716	-0.0371	0.119	-0.0312	0.1214	-0.0122	0.0432	0.261	0.003	0.2864	17.1523	-18.1943	-18.4055
16	8.1417	-2.7115	3.6045	7.6326	-2.3481	5.75	-0.4537	-0.3127	0.6115	0.0946	0.0664	0.2562	-0.0921	-0.6962	0.4673	0.3043	0.0544	0.0657	0.244	-0.0103	0.3918	10.0671	-4.2284	-13.5178
17	6.3348	3.849	5.0084	5.2043	5.0379	8.5347	-0.0392	0.6789	0.0774	-0.6389	0.2769	-0.7229	-0.7668	0.6289	-0.1931	0.2708	-0.0222	0.0234	0.3954	0.1144	0.4466	13.9028	-3.6455	-23.8397
18	6.8711	0.1606	0.9472	2.4159	0.5779	5.5721	0.056	0.5554	0.3044	-0.1935	0.1053	-0.2927	-0.633	0.5292	-0.1366	0.1754	0.0065	0.0417	0.2368	0.0449	0.3052	17.7224	-9.729	-20.3269
19	1.9713	-0.9174	1.0715	2.6641	-0.5118	5.8357	-0.0619	0.2258	0.0814	0.1458	0.0701	-0.4659	-0.7883	0.7607	-0.1042	0.1859	-0.0283	0.0301	0.3206	0.0058	0.3764	25.6337	-15.2815	-15.8203
20	3.0002	-0.4245	0.6134	2.736	-1.6335	7.1487	0.037	-0.1843	-0.0166	0.2871	0.04	0.2676	-0.4062	0.2867	0.019	0.1107	-0.0057	0.0623	0.28	-0.0112	0.2623	14.2701	-13.2418	-10.1124
21	0.4606	-0.2255	0.6695	0.9742	0.0943	1.2157	0.1935	0.1169	0.0436	0.1906	-0.0815	0.4499	-0.0939	-0.6501	-0.0307	0.073	0.0105	0.0166	0.3527	0.0524	0.2257	10.569	-17.1262	-10.4218
22	5.3175	-0.0278	-2.5648	2.6332	0.7418	4.6675	0.4426	0.1967	1.6756	-0.1502	0.02	-0.4561	-0.695	0.1792	-0.3483	0.2321	-0.0045	0.0345	0.3114	0.0693	0.5172	14.2112	-33.5575	-18.2463
23	6.3637	2.6947	4.879	3.1777	2.0363	3.738	0.0159	-0.6585	1.8426	0.1792	-0.1529	0.6803	-0.4524	-1.3404	0.3058	0.2778	0.0827	-0.0015	0.563	-0.0315	0.449	-0.4429	-34.3242	-7.194
24	6.6853	0.1186	-2.329	1.9142	0.4011	4.1901	-0.0565	0.4432	0.1123	0.0654	0.0138	-0.2241	0.2933	-0.2338	0.0465	0.1726	-0.0171	-0.023	0.2013	-0.0424	0.2552	13.7737	-43.3845	-18.16
25	5.0491	0.552	-1.984	2.2456	1.1816	1.8939	-0.2786	0.7909	-0.6478	-0.0008	-0.014	-0.059	0.9089	-0.6811	0.1371	0.3494	-0.1116	0.02	0.3233	-0.0761	0.3552	11.5143	-49.9607	-20.4288
26	4.6131	-0.1502	-0.4991	0.6253	0.2539	4.9183	-0.0213	-0.0539	-0.1373	0.1339	0.0095	0.1531	0.4777	-1.1315	0.1156	0.2899	-0.0644	0.0066	0.3505	-0.0152	0.3727	1.9897	-41.6499	-10.0801
27	5.234	-0.9521	-2.4009	2.6512	1.6744	5.0943	-0.1296	-0.1762	-0.0946	0.0802	0.0149	-0.207	0.2385	0.3314	0.064	0.1833	-0.0008	-0.0229	0.2093	0.0304	0.2543	15.1288	-40.7687	-11.2341

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 1 through 8 )	A	1 - 8
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 18 )	A	9 - 18
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 19 through 27 )	A	19 - 27
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 28 through 40 )	A	28 - 40
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 41 through 55 )	A	41 - 55
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 56 through 85 )	A	56 - 85
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 86 through 101 )	A	86 - 101
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 102 through 107 )	A	102 - 107
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 108 through 128 )	A	108 - 128
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 34 )	B	3 - 34
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 35 through 64 )	B	35 - 64
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 65 through 107 )	B	65 - 107
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 128 )	B	108 - 128
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3 through 18 )	C	3 - 18
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 19 through 52 )	C	19 - 52
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 53 through 66 )	C	53 - 66
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 67 through 75 )	C	67 - 75
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 76 through 91 )	C	76 - 91
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 92 through 101 )	C	92 - 101
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 102 through 116 )	C	102 - 116
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 117 through 127 )	C	117 - 127
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 18 )	D	3 - 18
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 19 through 27 )	D	19 - 27
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 28 through 64 )	D	28 - 64
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 65 through 91 )	D	65 - 91
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 92 through 107 )	D	92 - 107
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 108 through 128 )	D	108 - 128

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