PDB-5mjo: Structure of Psb29 at 1.55A

ID or keywords:

Entry

Database: PDB / ID: 5mjo

Title

Structure of Psb29 at 1.55A

Components

Protein Thf1

Keywords

PHOTOSYNTHESIS /

photosystem II FtsH

Function / homology

Protein Thf1 / Thylakoid formation protein /

photosystem II assembly /

: / IODIDE ION / Protein Thf1

Function and homology information

Biological species

Thermosynechococcus elongatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Murray, J.W. / Kozlo, A.

Funding support

United Kingdom, 2items

Citation

Journal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2017
Title: Structure of Psb29/Thf1 and its association with the FtsH protease complex involved in photosystem II repair in cyanobacteria.
Authors: Bec Kova, M. / Yu, J. / Krynicka, V. / Kozlo, A. / Shao, S. / Konik, P. / Komenda, J. / Murray, J.W. / Nixon, P.J.

History

Deposition	Dec 1, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5mjo.cif.gz	97.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjo ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjo	HTTPS FTP

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Related structure data

Related structure data	5mjrC 5mjwC 5mlfC C: citing same article (ref.)
Similar structure data	2vv6-1 5mjr-d 3kv0-d 2vv6-2 4k8n-5 3bcw-d 5tss-1 4kbs-2 1cz4-d 4kbr-8 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	#147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Protein Thf1

hetero molecules

27.7 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)	31.240, 56.730, 47.730
Angle α, β, γ (deg.)	90.00, 104.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein Thf1 Mass: 27268.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Gene: thf1, tlr1134 / Plasmid: pRSETa modified / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q8DJT8
#2: Chemical	ChemComp-HG / MERCURY (II) ION / Mercury (element) Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.95 Å³/Da / Density % sol: 37 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Bicine, pH 9.0, 20% w/v PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9173 Å / Relative weight: 1
Reflection	Resolution: 1.55→46.16 Å / Num. obs: 23219 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.9 % / B_iso Wilson estimate: 15.949 Å² / R_merge(I) obs: 0.114 / Net I/av σ(I): 18.3675 / Net I/σ(I): 5.2976
Reflection shell	Resolution: 1.55→1.59 Å / Redundancy: 16.68 % / R_merge(I) obs: 1.098 / Mean I/σ(I) obs: 0.65 / % possible all: 99.17

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
xia2		data reduction
xia2		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→46.16 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / SU B: 3.561 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19243	1187	5.1 %	RANDOM
R_work	0.13321	-	-	-
obs	0.13631	22013	98.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 18.479 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	0.02 Å²
2-	-	-0.15 Å²	-0 Å²
3-	-	-	0.3 Å²

Refinement step

Cycle: 1 / Resolution: 1.55→46.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1507	0	3	110	1620

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.019	1559
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1433
X-RAY DIFFRACTION	r_angle_refined_deg	2.07	1.957	2118
X-RAY DIFFRACTION	r_angle_other_deg	1.17	3	3326
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.057	5	191
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.3	23.827	81
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.068	15	265
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.643	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.145	0.2	233
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1738
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	323
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	2.985	1.322	752
X-RAY DIFFRACTION	r_mcbond_other	2.933	1.315	751
X-RAY DIFFRACTION	r_mcangle_it	3.546	1.983	941
X-RAY DIFFRACTION	r_mcangle_other	3.581	1.987	942
X-RAY DIFFRACTION	r_scbond_it	5.385	1.899	807
X-RAY DIFFRACTION	r_scbond_other	5.383	1.901	808
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.009	2.661	1176
X-RAY DIFFRACTION	r_long_range_B_refined	5.248	17.119	1790
X-RAY DIFFRACTION	r_long_range_B_other	5.226	16.982	1780
X-RAY DIFFRACTION	r_rigid_bond_restr	4.505	3	2992
X-RAY DIFFRACTION	r_sphericity_free	21.688	5	69
X-RAY DIFFRACTION	r_sphericity_bonded	13.092	5	2998

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	72	-
R_work	0.147	1627	-
obs	-	-	99.01 %

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	3.9664	1.8202	-1.9013	2.4204	-0.3613	1.0763	0.1304	-0.1313	0.1871	-0.0267	-0.0479	0.1054	-0.0887	0.067	-0.0825	0.023	-0.0055	0.0037	0.0135	-0.01	0.011	15.143	22.3585	1.4612
2	0.2854	0.3384	-0.0437	0.6585	0.182	0.2194	0.0117	-0.0214	-0.0057	0.0328	0.0033	-0.0264	0.0186	0.0275	-0.0151	0.031	0.0012	-0.0071	0.0068	-0	0.0036	9.2906	8.8478	6.8393
3	0.5362	1.1482	-0.4469	3.8296	-0.9368	0.573	0.0029	-0.0183	-0.0207	0.0381	-0.0222	-0.0904	0.0214	0.0368	0.0194	0.0213	0.0032	-0.0015	0.0034	0.0007	0.0026	10.6918	10.9943	-3.8067
4	0.7127	0.5558	-0.2411	0.4472	-0.2293	0.2061	0.0424	-0.0105	0.0194	0.0448	-0.0125	0.0202	-0.0331	-0.0002	-0.0298	0.0346	0.0022	-0.0025	0.0014	0.0006	0.0086	4.5283	24.3139	-11.5178
5	0.0451	-0.1665	0.1572	0.6332	-0.6065	0.5866	-0.0021	0.0025	-0.001	0.0206	0.0008	0.0005	-0.0195	-0.0078	0.0013	0.0325	-0.0019	-0.002	0.0088	-0.0015	0.0029	-0.0202	6.2278	-3.8675
6	0.5783	-0.0739	1.0519	3.236	-0.8888	2.0932	0.0947	-0.0624	-0.0347	0.041	0.0062	0.1669	0.1456	-0.114	-0.1009	0.0435	-0.0056	0.0019	0.0094	0.0029	0.0122	0.2667	9.949	3.5438
7	0.3472	0.0591	0.2641	0.0122	0.0389	0.2214	0.0121	-0.0095	-0.0088	0.0028	-0.0029	-0.0017	0.0168	-0.0094	-0.0092	0.0288	0.0004	-0.0016	0.0042	0.0008	0.0046	-5.2064	17.2473	-5.8296
8	0.0239	-0.044	-0.0292	0.2051	-0.0424	0.1133	0.0032	-0.0014	-0.0007	-0.0177	0.0039	0.0111	-0.0068	-0.0012	-0.0071	0.0298	0.0014	-0.0039	0.0039	0.0019	0.0032	-10.8983	18.8168	-24.342
9	0.3366	0.2687	0.034	0.2733	0.0847	0.0613	-0.0052	-0.0076	0.0123	-0.0145	-0.003	0.0151	-0.0051	0.0016	0.0082	0.0284	-0.0004	-0.0027	0.0015	0	0.005	-0.7226	13.461	-18.7117
10	0.0713	-0.1064	0.0202	0.2059	0.0001	0.0316	-0.006	0.001	0.0017	0.0005	0.0041	-0.0015	0.0057	0.0031	0.0018	0.0299	-0.0008	-0.0005	0.0022	0	0.0024	3.3755	7.8198	-23.5011

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 9
2	X-RAY DIFFRACTION	2	A	10 - 25
3	X-RAY DIFFRACTION	3	A	26 - 41
4	X-RAY DIFFRACTION	4	A	42 - 51
5	X-RAY DIFFRACTION	5	A	52 - 72
6	X-RAY DIFFRACTION	6	A	73 - 80
7	X-RAY DIFFRACTION	7	A	81 - 102
8	X-RAY DIFFRACTION	8	A	103 - 125
9	X-RAY DIFFRACTION	9	A	126 - 149
10	X-RAY DIFFRACTION	10	A	150 - 189

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