PDB-2y6x: Structure of Psb27 from Thermosynechococcus elongatus

ID or keywords:

Entry

Database: PDB / ID: 2y6x

Title

Structure of Psb27 from Thermosynechococcus elongatus

Components

PHOTOSYSTEM II 11 KD PROTEIN

Keywords

PHOTOSYNTHESIS

Function / homology

Function and homology information

photosystem II repair /

thylakoid lumen /

thylakoid /

photosystem II assembly /

photosystem II / plasma membrane-derived thylakoid membrane
Similarity search - Function

Biological species

THERMOSYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Michoux, F. / Takasaka, K. / Boehm, M. / Nixon, P.J. / Murray, J.W.

Citation

Journal: Photosynth.Res. / Year: 2012
Title: Crystal Structure of the Psb27 Assembly Factor at 1.6A: Implications for Binding to Photosystem II.
Authors: Michoux, F. / Takasaka, K. / Boehm, M. / Komenda, J. / Nixon, P.J. / Murray, J.W.

History

Deposition	Jan 27, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2012	Group: Other
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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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PDBx/mmCIF format	2y6x.cif.gz	62.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6x ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6x	HTTPS FTP

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Related structure data

Related structure data	2kmfS S: Starting model for refinement
Similar structure data	3njf-3 4ahi-d 7nq8-d 3n55-d 3i3j-7 3hvp-d 4qfi-1 6igw-d 3euy-2 3njj-d 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: PHOTOSYSTEM II 11 KD PROTEIN

hetero molecules

12.7 kDa, 1 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)	36.930, 50.820, 53.070
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PHOTOSYSTEM II 11 KD PROTEIN / / PSB27 Mass: 12689.293 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Plasmid: PRSET-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): KRX / References: UniProt: Q8DG60
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.03 Å³/Da / Density % sol: 39.35 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop Details: 35% W/V PEG 4K MIXED WITH EQUAL VOLUME OF 20MG/ML PROTEIN SOLUTION, HANGING DROP VAPOUR DIFFUSION

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2831
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 30, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2831 Å / Relative weight: 1
Reflection	Resolution: 1.6→30.31 Å / Num. obs: 13700 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.52 % / R_merge(I) obs: 0.07 / Net I/σ(I): 8.31
Reflection shell	Resolution: 1.6→1.69 Å / Redundancy: 6.61 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 3.16 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0104	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KMF

2kmf

Resolution: 1.6→30.31 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.931 / SU B: 4.004 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23775	683	5 %	RANDOM
R_work	0.1901	-	-	-
obs	0.19246	12980	99.73 %	-

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 mean: 16.831 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0 Å²
2-	-	-0.14 Å²	0 Å²
3-	-	-	0.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	867	0	1	130	998

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	913
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	657
X-RAY DIFFRACTION	r_angle_refined_deg	1.892	1.988	1235
X-RAY DIFFRACTION	r_angle_other_deg	1.026	3	1597
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.627	5	116
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.278	23.778	45
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.628	15	169
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.266	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	134
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	1029
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	188
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	215
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	625
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	443
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	511
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	55
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.089	0.2	511
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.178	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.13	0.2	15
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	1.108	1.5	566
X-RAY DIFFRACTION	r_mcbond_other	0.4	1.5	223
X-RAY DIFFRACTION	r_mcangle_it	1.778	2	908
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.207	3	347
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.334	4.5	325
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	58	-
R_work	0.275	913	-
obs	-	-	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	4.5265	0.5827	-1.9999	0.7617	-0.0675	2.1268	-0.0133	-0.1321	-0.1036	0.1096	-0.0184	0.0004	0.0722	0.0182	0.0317	0.0241	-0.0018	-0.0097	0.0328	0.0163	0.0344	6.359	-2.429	8.797
2	4.7078	0.7248	-4.1665	0.7814	-0.2763	3.945	0.1155	0.1382	0.2412	0.0473	0.0328	0.1039	-0.1271	-0.1722	-0.1483	0.0348	0.0336	-0.0193	0.0817	-0.0025	0.0504	4.035	6.248	8.586
3	1.9549	1.2911	0.4464	1.5056	1.7067	5.9901	-0.0371	0.2758	0.3627	-0.2974	0.2105	-0.0914	-0.6968	0.4018	-0.1734	0.1247	0.0011	0.108	0.1501	0.0769	0.3086	16.272	6.309	-5.363
4	8.7013	-4.0182	-2.7122	2.4765	1.4001	1.1351	0.1534	0.1057	0.1782	-0.1277	-0.0395	0.0462	-0.1182	-0.1114	-0.1139	0.0293	0.0058	0.014	0.0464	0.0278	0.0614	0.214	5.019	-1.268
5	4.5682	-2.4035	-2.2335	3.6618	1.1307	1.1117	-0.0749	0.1019	-0.1589	0.016	0.0401	0.203	0.0398	-0.0836	0.0348	0.005	-0.0183	-0.0086	0.0965	0.0286	0.0856	-8.198	-1.849	0.952
6	13.5651	-2.513	-2.4545	2.1332	-0.4056	2.2818	-0.041	0.214	-0.5462	-0.0838	-0.0021	0.0826	0.3692	-0.0538	0.0431	0.0766	-0.0031	-0.0116	0.008	-0.0108	0.0259	10.361	-9.005	-3.767
7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.029	0	0	0.029	0	0.029	0	0	0
8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.029	0	0	0.029	0	0.029	0	0	0
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.029	0	0	0.029	0	0.029	0	0	0
10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.029	0	0	0.029	0	0.029	0	0	0
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.029	0	0	0.029	0	0.029	0	0	0
12	21.7836	-0.6344	-28.1472	31.8752	0.4088	65.4667	0.6811	-0.0939	0.6763	-0.1321	0.062	-0.9925	0.4714	1.7973	-0.7431	0.1562	0.0217	0.0051	0.1507	-0.0009	0.0908	22.72	-9.751	-9.21

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 55
2	X-RAY DIFFRACTION	2	A	56 - 75
3	X-RAY DIFFRACTION	3	A	76 - 85
4	X-RAY DIFFRACTION	4	A	86 - 105
5	X-RAY DIFFRACTION	5	A	106 - 118
6	X-RAY DIFFRACTION	6	A	119 - 133
7	X-RAY DIFFRACTION	7	A	27 - 55
8	X-RAY DIFFRACTION	8	A	56 - 75
9	X-RAY DIFFRACTION	9	A	76 - 85
10	X-RAY DIFFRACTION	10	A	86 - 105
11	X-RAY DIFFRACTION	11	A	106 - 118
12	X-RAY DIFFRACTION	12	A	119 - 134

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