PDB-6mez: X-ray structure of the Fenna-Matthews-Olsen antenna complex from ...

ID or keywords:

Entry

Database: PDB / ID: 6mez

Title

X-ray structure of the Fenna-Matthews-Olsen antenna complex from Prosthecochloris aestuarii

Components

Bacteriochlorophyll a protein

Keywords

PHOTOSYNTHESIS / FMO Photosynthesis Antenna complex / Energy transfer

Function / homology

Function and homology information

bacteriochlorophyll binding / photosynthesis / metal ion binding
Similarity search - Function

Biological species

Prosthecochloris aestuarii (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 1.74 Å

Authors

Selvaraj, B. / Lu, X. / Cuneo, M.J. / Myles, D.A.A.

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Neutron and X-ray analysis of the Fenna-Matthews-Olson photosynthetic antenna complex from Prosthecochloris aestuarii.
Authors: Lu, X. / Selvaraj, B. / Ghimire-Rijal, S. / Orf, G.S. / Meilleur, F. / Blankenship, R.E. / Cuneo, M.J. / Myles, D.A.A.

History

Deposition	Sep 7, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6mez.cif.gz	342.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6mez.ent.gz	287 KB	Display	PDB format
PDBx/mmJSON format	6mez.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6mez_validation.pdf.gz	4.8 MB	Display	wwPDB validaton report
Full document	6mez_full_validation.pdf.gz	4.8 MB	Display
Data in XML	6mez_validation.xml.gz	37.9 KB	Display
Data in CIF	6mez_validation.cif.gz	54.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/me/6mez ftp://data.pdbj.org/pub/pdb/validation_reports/me/6mez	HTTPS FTP

-
Related structure data

Related structure data	6e9j PDB Unreleased entry
Similar structure data	3eoj-1 3bsd-1 5h8z-2 4bcl-1 3vdi-1 1xiv-1 3eni-2 1u5a-1 1ez4-d 5h8z-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bacteriochlorophyll a protein

B: Bacteriochlorophyll a protein

hetero molecules

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

1

A: Bacteriochlorophyll a protein

hetero molecules

A: Bacteriochlorophyll a protein

hetero molecules

A: Bacteriochlorophyll a protein

hetero molecules

defined by author&software
Evidence: assay for oligomerization
139 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Bacteriochlorophyll a protein

hetero molecules

B: Bacteriochlorophyll a protein

hetero molecules

B: Bacteriochlorophyll a protein

hetero molecules

defined by author&software
139 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.638, 83.638, 294.781
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-606- HOH
2	1	A-653- HOH
3	1	B-551- HOH
4	1	B-692- HOH
5	1	B-735- HOH

#1: Protein	Bacteriochlorophyll a protein / BChl a protein Mass: 39663.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prosthecochloris aestuarii (bacteria) / Production host: Prosthecochloris aestuarii (bacteria) / References: UniProt: P11741
#2: Chemical	ChemComp-BCL / BACTERIOCHLOROPHYLL A Mass: 911.504 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₅₅H₇₄MgN₄O₆
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.06 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 8 Details: 25 % Ammonium Sulfate and 0.1 M Sodium acetate pH 5.0

-
Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5417 Å / Relative weight: 1
Reflection	Resolution: 1.74→19.65 Å / Num. obs: 73467 / % possible obs: 93.3 % / Redundancy: 3.6 % / R_merge(I) obs: 0.061 / Net I/av σ(I): 10.8 / Net I/σ(I): 2.4
Reflection shell	Resolution: 1.74→1.804 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.409 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3850 / % possible all: 49.16

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.74→19.65 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.6
Details: Molecular replacement was done using 3EOJ as a starting model.

	R_factor	Num. reflection	% reflection
R_free	0.1586	3693	5.03 %
R_work	0.1323	-	-
obs	0.1336	73454	93.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.74→19.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5530	0	954	474	6958

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	7699
X-RAY DIFFRACTION	f_angle_d	1.297	10835
X-RAY DIFFRACTION	f_dihedral_angle_d	13.516	2858
X-RAY DIFFRACTION	f_chiral_restr	0.066	1085
X-RAY DIFFRACTION	f_plane_restr	0.006	1437

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7415-1.7644	0.2145	44	0.1887	881	X-RAY DIFFRACTION	31
1.7644-1.7885	0.237	80	0.1876	1564	X-RAY DIFFRACTION	54
1.7885-1.8141	0.2389	119	0.1826	2181	X-RAY DIFFRACTION	76
1.8141-1.8411	0.1887	132	0.1701	2485	X-RAY DIFFRACTION	88
1.8411-1.8699	0.2155	150	0.1596	2714	X-RAY DIFFRACTION	94
1.8699-1.9005	0.2011	129	0.156	2801	X-RAY DIFFRACTION	97
1.9005-1.9332	0.1729	149	0.148	2806	X-RAY DIFFRACTION	98
1.9332-1.9684	0.1688	173	0.1443	2824	X-RAY DIFFRACTION	99
1.9684-2.0062	0.1794	150	0.1449	2834	X-RAY DIFFRACTION	99
2.0062-2.0471	0.174	137	0.1414	2882	X-RAY DIFFRACTION	99
2.0471-2.0916	0.1785	123	0.1395	2867	X-RAY DIFFRACTION	99
2.0916-2.1401	0.1651	147	0.1365	2834	X-RAY DIFFRACTION	99
2.1401-2.1936	0.1565	150	0.1347	2896	X-RAY DIFFRACTION	99
2.1936-2.2528	0.1726	156	0.1373	2848	X-RAY DIFFRACTION	100
2.2528-2.319	0.1598	146	0.1349	2843	X-RAY DIFFRACTION	100
2.319-2.3937	0.1646	155	0.1403	2872	X-RAY DIFFRACTION	100
2.3937-2.4791	0.1803	136	0.1468	2896	X-RAY DIFFRACTION	100
2.4791-2.5782	0.1796	155	0.1466	2836	X-RAY DIFFRACTION	100
2.5782-2.6953	0.16	142	0.1487	2913	X-RAY DIFFRACTION	100
2.6953-2.837	0.191	161	0.1442	2824	X-RAY DIFFRACTION	100
2.837-3.0141	0.1741	156	0.1488	2889	X-RAY DIFFRACTION	100
3.0141-3.2459	0.1738	163	0.1366	2837	X-RAY DIFFRACTION	100
3.2459-3.5708	0.1601	168	0.1195	2875	X-RAY DIFFRACTION	100
3.5708-4.0834	0.12	148	0.1046	2857	X-RAY DIFFRACTION	100
4.0834-5.1295	0.102	152	0.0968	2845	X-RAY DIFFRACTION	99
5.1295-19.6533	0.145	172	0.1236	2857	X-RAY DIFFRACTION	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	-0.0023	-0.0008	-0.0031	0.0007	-0.0047	0.0042	0.0263	-0.0087	-0.017	0.0177	0.0064	0.0031	0.0163	-0.0194	-0	0.1545	0.005	0.0304	0.0691	0.0494	0.0218	-7.8392	27.1104	-50.52
2	0.002	0.0037	-0.0015	0.0067	-0.005	0.0023	0.0035	-0.0042	-0.0136	0.0171	0.0131	0.0029	0.0223	-0.0318	0	0.0796	-0.0134	0.0147	0.0712	-0.011	0.072	-14.9654	23.2844	-72.2142
3	-0.0004	-0.0006	-0	0.0005	0.0001	0.0004	-0.0139	0.0013	-0.0076	-0.0062	-0.0015	0.0013	0.005	0.0023	-0	0.0928	0.0204	0.005	0.0584	0.0158	0.0686	15.5738	27.1067	-72.2695
4	0.0024	0.0023	0.0012	0.0035	0.0024	0.0011	0.0092	0.018	0.0089	-0.0022	0.0268	0.0228	-0.0214	-0.0173	0	0.0485	-0.0041	-0.0248	0.0759	0.0113	0.0485	-15.6515	38.9365	-81.4164
5	0.0004	0.002	-0.0015	-0.0002	-0.0013	0.0025	0.0041	0.0177	-0.0094	0.0054	0.0008	0.016	-0.0002	-0.0138	-0	0.0516	-0.0047	-0.0086	0.0919	-0.0038	0.0572	-13.673	32.4097	-85.8992
6	0	-0.0004	0.0004	0.0006	0.0005	0.0006	0.0006	-0.0007	-0.0114	0.0025	0.0028	0.0025	0.0099	0.0088	0	0.1109	-0.0027	-0.0125	0.0343	0.0128	0.059	0.2068	21.1551	-69.0292
7	-0.0057	-0.0008	0.0002	0.0015	-0.0077	0.0032	-0.0082	-0.0313	-0.035	0.0374	-0.0342	0.0093	0.0006	-0.0044	0	0.1003	-0.0093	0.0314	0.0033	0.0921	-0.0877	-4.184	28.7238	-53.8163
8	-0.0038	-0.0033	0.0002	0.0001	-0.0023	0.0017	0.0102	-0.0397	-0.0607	0.0154	-0.0119	-0.0192	0.0234	0.0015	0	0.1343	-0.0063	-0.0317	-0.0057	0.1455	-0.0393	7.3772	23.7483	-46.8726
9	0.001	0.0012	-0.0048	0.0004	0.0023	-0.0008	0.0101	0.0276	-0.0153	-0.0191	0.0255	-0.0432	-0.0007	0.0112	0	-0.02	0.0383	0.0806	0.0284	-0.0233	0.0155	-20.2401	28.181	-32.0752
10	0.0009	0.0024	0.0006	0.0021	0.0011	0.0002	0.0139	0.0012	0.0016	0.0023	0.009	-0.0087	-0.0061	0.0054	-0	0.0575	0.0196	-0.0069	0.0824	-0.0149	0.1403	-9.3426	32.4521	-16.5584
11	0.0019	0.0018	0.0008	0.0001	-0.0021	-0.0015	0.0235	0.0159	0.0058	0.0025	0.0344	-0.0147	-0.0004	0.011	-0	0.0507	0.0057	-0.0081	0.0639	-0.0092	0.1268	-14.7285	36.1586	-12.9207
12	0.0032	0.0008	0.0003	0.0006	-0.0007	-0.0004	0.0234	0.002	0.0134	0.0028	0.014	-0.0054	-0.007	-0.0162	-0	0.0277	-0.0133	-0.044	0.0374	-0.0416	0.1176	-16.7572	33.6484	-4.3073
13	0.009	-0.0038	0.0007	0.0006	-0.0005	-0	-0.0164	-0.0418	0.0024	0.0068	-0.017	-0.0236	0.0025	0.0025	-0	0.0412	-0.0005	-0.021	0.0349	-0.0146	0.0741	-22.9455	16.4784	-5.5695
14	-0.0005	0.0009	0.001	0.0003	0.0002	-0.0005	0.0064	-0.0301	0.0277	0.0042	0.0185	-0.0063	-0.0084	-0.0199	-0	0.0155	0.0005	-0.042	0.0315	-0.1136	0.0077	-31.7877	42.4975	2.5516
15	0.001	-0.0016	-0.0017	0.0012	0.0007	0.0006	0.0043	-0.0052	0.0216	0.0112	0.0164	-0.0083	-0.0069	-0.0095	-0	0.0189	-0.0218	-0.0137	0.006	-0.0235	0.0008	-28.8337	33.2332	-2.9195
16	0.0008	0.0019	0.0012	0.0024	-0.0027	0.0013	-0.0045	-0.0024	0.0149	-0.0031	-0.0006	-0.061	0.0203	0.0008	-0	-0.0164	0.0044	-0.021	-0.0147	-0.0652	0.0196	-17.7753	24.3487	-7.2274
17	0.0026	-0.0032	-0.002	0	0.0035	-0.0001	-0.0097	0.0378	0.0035	-0.0197	0.0219	-0.0574	0.0102	-0.0157	-0	-0.0696	0.0614	0.1063	0.0077	-0.0422	-0.03	-22.1677	24.7911	-28.6286
18	-0.0014	-0.0054	-0.0021	-0.0046	0.0008	-0.0004	-0.0137	0.0307	-0.0243	-0.032	0.0222	-0.0534	-0.0001	0.0255	-0	-0.1616	0.1176	0.2129	-0.0051	-0.1295	-0.1118	-19.1338	12.3727	-35.8377

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 196 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 197 through 229 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 230 through 251 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 252 through 316 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 317 through 366 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 7 through 45 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 46 through 62 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 63 through 93 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 94 through 122 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 123 through 155 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 156 through 184 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 185 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 251 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 252 through 316 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 317 through 366 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi