PDB-3ls1: Crystal Structure of Cyanobacterial PsbQ from Synechocystis sp. P...

ID or keywords:

Entry

Database: PDB / ID: 3ls1

Title

Crystal Structure of Cyanobacterial PsbQ from Synechocystis sp. PCC 6803 complexed with Zn2+

Components

Sll1638 protein

Keywords

PHOTOSYNTHESIS / Four helix bundle

Function / homology

Function and homology information

plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / photosynthesis / calcium ion binding
Similarity search - Function

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Jackson, S.A. / Fagerlund, R.D. / Wilbanks, S.M. / Eaton-Rye, J.J.

Citation

Journal: Biochemistry / Year: 2010
Title: Crystal Structure of PsbQ from Synechocystis sp. PCC 6803 at 1.8 A: Implications for Binding and Function in Cyanobacterial Photosystem II
Authors: Jackson, S.A. / Fagerlund, R.D. / Wilbanks, S.M. / Eaton-Rye, J.J.

History

Deposition	Feb 12, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 31, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site 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_atom_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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	3ls1.cif.gz	124 KB	Display	PDBx/mmCIF format
PDB format	pdb3ls1.ent.gz	97.3 KB	Display	PDB format
PDBx/mmJSON format	3ls1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ls1_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	3ls1_full_validation.pdf.gz	444.3 KB	Display
Data in XML	3ls1_validation.xml.gz	15.4 KB	Display
Data in CIF	3ls1_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ls/3ls1 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3ls1	HTTPS FTP

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Related structure data

Related structure data	3ls0SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ncx-1 2624 5ziy-1 2xze-1 5m9e-1 2cpc-d 2vrz-d 5m9e-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Sll1638 protein

B: Sll1638 protein

hetero molecules

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

1

A: Sll1638 protein

hetero molecules

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

2

B: Sll1638 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.771, 29.030, 99.503
Angle α, β, γ (deg.)	90.00, 97.77, 90.00
Int Tables number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 17 - 149 / Label seq-ID: 1 - 133

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Sll1638 protein / PsbQ Mass: 14608.493 Da / Num. of mol.: 2 / Fragment: residues 21-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: sll1638 / Plasmid: pGEX-6-P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73048
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.27 Å³/Da / Density % sol: 45.86 % / Mosaicity: 0.69 °
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 1450, 0.1M MES-NaOH, pH 6.5, 0.05M ZINC CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 29, 2009 / Details: 0.3 MM OSMIC VARIMAX
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.85→21.76 Å / Num. obs: 22914 / % possible obs: 99.6 % / Redundancy: 8.5 % / R_merge(I) obs: 0.06 / Net I/σ(I): 20.4
Reflection shell	Resolution: 1.85→1.95 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.264 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3246 / % possible all: 97.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LS0

3ls0

Resolution: 1.85→21.76 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.937 / WR_factor R_free: 0.219 / WR_factor R_work: 0.178 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.84 / SU B: 5.929 / SU ML: 0.093 / SU R Cruickshank DPI: 0.145 / SU R_free: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	1175	5.1 %	RANDOM
R_work	0.179	-	-	-
obs	0.181	22914	99.59 %	-

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 max: 42.43 Å² / B_iso mean: 27.76 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.04 Å²	0 Å²	0.24 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→21.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2070	0	4	241	2315

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.022	2110
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.01	1.981	2865
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.046	5	272
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.451	25.556	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.276	15	370
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.584	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.182	0.2	320
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1614
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	1.162	1.5	1338
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.871	2	2146
X-RAY DIFFRACTION	r_scbond_it	3.36	3	772
X-RAY DIFFRACTION	r_scangle_it	5.174	4.5	715
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
531	medium positional	0.54	0.5
492	loose positional	0.75	5
531	medium thermal	0.86	2
492	loose thermal	1.27	10

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	73	-
R_work	0.285	1521	-
all	-	1594	-
obs	-	-	95.68 %

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	15.2167	-6.896	14.6204	3.1267	-6.6627	15.3953	-0.0093	0.0905	-0.1995	0.0066	-0.0312	0.086	-0.1177	0.0423	0.0406	0.3039	-0.0051	-0.0467	0.0821	0.02	0.1141	64.942	-4.041	31.504
2	8.0653	1.3556	5.6261	0.452	1.7726	7.0068	0.8898	0.561	-2.5254	0.1252	0.2432	-0.2942	0.4933	0.9301	-1.1329	0.2141	-0.0347	-0.3791	0.6063	0.3821	1.3632	44.435	-13.759	24.246
3	3.273	-1.6144	3.132	1.7338	-1.3665	4.4307	0.0293	0.0222	-0.1988	-0.0579	0.0139	0.0695	-0.047	0.0715	-0.0433	0.192	-0.0207	-0.0355	0.0896	-0.0015	0.0627	21.033	-9.957	19.877
4	4.9075	-0.3713	1.0915	1.6931	-0.0091	4.0903	0.1163	0.3141	-0.0791	-0.1334	-0.0291	0.1763	-0.1489	-0.4076	-0.0873	0.1841	0.0371	-0.0711	0.1324	0.0055	0.0425	9.103	-0.512	10.533
5	6.6999	-0.9111	0.5464	3.0588	0.3511	4.7571	-0.1813	-0.2266	0.2502	0.1008	-0.0133	-0.1203	-0.2338	0.2089	0.1946	0.1878	-0.0078	-0.0612	0.0878	-0.0093	0.0323	26.411	-1.059	19.188
6	6.079	-2.8838	1.6572	3.2861	-1.5798	3.9833	-0.142	-0.2769	0.2016	-0.0038	-0.0019	-0.3877	-0.08	0.4554	0.1438	0.1913	-0.0302	-0.0324	0.1482	0.0053	0.061	31.813	-3.794	12.465
7	5.9473	0.6673	-0.3454	4.6444	2.9748	7.5523	0.0881	0.6802	0.3264	-0.4201	-0.0648	-0.0811	-0.5754	-0.7826	-0.0234	0.2727	0.0558	-0.0688	0.2298	0.0423	0.0535	12.811	2.216	1.429
8	2.5198	-0.6536	1.6295	2.3913	-1.6807	5.4188	-0.0809	0.0334	-0.3744	-0.2031	0.0544	-0.0751	0.287	0.0502	0.0264	0.2306	-0.008	-0.0037	0.0862	-0.0055	0.0866	25.349	-10.985	10.115
9	7.9135	5.4474	8.9039	3.8869	5.3815	14.144	0.1831	0.0527	-0.6155	0.1426	-0.0249	-0.5179	0.0026	0.4025	-0.1581	0.2558	0.0082	-0.0242	0.1013	-0.0043	0.1891	-14.732	-6.256	-29.008
10	8.1403	0.1911	-6.4035	4.0751	-3.8401	9.1438	-0.1331	0.1352	-0.3244	-0.106	0.0611	0.3618	0.1463	-0.771	0.0719	0.2331	-0.0104	-0.0831	0.4964	-0.1109	0.0998	7.007	-14.068	-23.11
11	3.8211	1.7188	3.1323	1.0363	1.2412	4.1195	-0.0204	0.1	-0.1963	-0.0239	0.0195	-0.1153	0.0381	0.0019	0.0008	0.2678	0.001	-0.0458	0.0958	-0.0127	0.0379	27.677	-8.349	-18.866
12	6.0085	-1.2613	1.652	1.4753	-0.9473	4.8559	0.0414	-0.2353	0.013	0.0474	-0.0311	-0.0241	-0.1958	0.4178	-0.0103	0.2389	-0.0352	-0.0585	0.1354	0.0046	0.0158	38.736	0.547	-11.685
13	13.7183	-0.2413	0.2914	6.1447	-2.5927	3.9213	-0.0727	0.4082	0.6656	-0.1984	0.0245	0.1688	-0.3834	-0.2058	0.0481	0.1809	0.0153	-0.0529	0.0986	0.019	0.0486	21.094	0.82	-18.48
14	7.1167	2.3345	1.9044	1.9315	0.8778	4.5317	-0.2549	-0.0867	0.0522	-0.3305	-0.092	0.3146	-0.1306	-0.8535	0.347	0.2598	0.0219	-0.1019	0.2704	-0.0632	0.1021	11.921	-4.86	-13.255
15	7.4922	1.693	1.4084	2.2483	-0.2555	4.0537	-0.0445	-0.3136	0.3458	0.1205	-0.0267	0.1356	-0.5704	0.2088	0.0713	0.3097	-0.0116	-0.0388	0.1045	-0.0267	0.0261	32.55	3.988	-4.248
16	7.8577	3.7565	3.81	2.9806	2.4324	5.5423	-0.028	-0.0364	-0.3699	0.0851	0.0227	-0.0897	0.2988	-0.18	0.0054	0.2703	0.0156	-0.0268	0.0915	-0.0052	0.0385	23.583	-9.423	-8.858

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 24
2	X-RAY DIFFRACTION	2	A	25 - 37
3	X-RAY DIFFRACTION	3	A	38 - 59
4	X-RAY DIFFRACTION	4	A	60 - 80
5	X-RAY DIFFRACTION	5	A	81 - 89
6	X-RAY DIFFRACTION	6	A	90 - 113
7	X-RAY DIFFRACTION	7	A	114 - 129
8	X-RAY DIFFRACTION	8	A	130 - 149
9	X-RAY DIFFRACTION	9	B	17 - 27
10	X-RAY DIFFRACTION	10	B	28 - 40
11	X-RAY DIFFRACTION	11	B	41 - 59
12	X-RAY DIFFRACTION	12	B	60 - 80
13	X-RAY DIFFRACTION	13	B	81 - 88
14	X-RAY DIFFRACTION	14	B	89 - 106
15	X-RAY DIFFRACTION	15	B	107 - 127
16	X-RAY DIFFRACTION	16	B	128 - 149

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Yorodumi