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- PDB-5mjo: Structure of Psb29 at 1.55A -

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Basic information

Entry
Database: PDB / ID: 5mjo
TitleStructure of Psb29 at 1.55A
ComponentsProtein Thf1
KeywordsPHOTOSYNTHESIS / photosystem II FtsH
Function / homologyProtein Thf1 / Thylakoid formation protein / plasma membrane-derived thylakoid photosystem II / photosystem II assembly / : / IODIDE ION / Protein Thf1
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMurray, J.W. / Kozlo, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I00937X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L003260/1 United Kingdom
CitationJournal: 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
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7234
Polymers27,2691
Non-polymers4543
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-28 kcal/mol
Surface area10040 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

#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


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 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

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

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→46.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.19243 1187 5.1 %RANDOM
Rwork0.13321 ---
obs0.13631 22013 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.02 Å2
2---0.15 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.55→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 3 110 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191559
X-RAY DIFFRACTIONr_bond_other_d0.0020.021433
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9572118
X-RAY DIFFRACTIONr_angle_other_deg1.1733326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0575191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.323.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06815265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6431513
X-RAY DIFFRACTIONr_chiral_restr0.1450.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211738
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9851.322752
X-RAY DIFFRACTIONr_mcbond_other2.9331.315751
X-RAY DIFFRACTIONr_mcangle_it3.5461.983941
X-RAY DIFFRACTIONr_mcangle_other3.5811.987942
X-RAY DIFFRACTIONr_scbond_it5.3851.899807
X-RAY DIFFRACTIONr_scbond_other5.3831.901808
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0092.6611176
X-RAY DIFFRACTIONr_long_range_B_refined5.24817.1191790
X-RAY DIFFRACTIONr_long_range_B_other5.22616.9821780
X-RAY DIFFRACTIONr_rigid_bond_restr4.50532992
X-RAY DIFFRACTIONr_sphericity_free21.688569
X-RAY DIFFRACTIONr_sphericity_bonded13.09252998
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 72 -
Rwork0.147 1627 -
obs--99.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.96641.8202-1.90132.4204-0.36131.07630.1304-0.13130.1871-0.0267-0.04790.1054-0.08870.067-0.08250.023-0.00550.00370.0135-0.010.01115.14322.35851.4612
20.28540.3384-0.04370.65850.1820.21940.0117-0.0214-0.00570.03280.0033-0.02640.01860.0275-0.01510.0310.0012-0.00710.0068-00.00369.29068.84786.8393
30.53621.1482-0.44693.8296-0.93680.5730.0029-0.0183-0.02070.0381-0.0222-0.09040.02140.03680.01940.02130.0032-0.00150.00340.00070.002610.691810.9943-3.8067
40.71270.5558-0.24110.4472-0.22930.20610.0424-0.01050.01940.0448-0.01250.0202-0.0331-0.0002-0.02980.03460.0022-0.00250.00140.00060.00864.528324.3139-11.5178
50.0451-0.16650.15720.6332-0.60650.5866-0.00210.0025-0.0010.02060.00080.0005-0.0195-0.00780.00130.0325-0.0019-0.0020.0088-0.00150.0029-0.02026.2278-3.8675
60.5783-0.07391.05193.236-0.88882.09320.0947-0.0624-0.03470.0410.00620.16690.1456-0.114-0.10090.0435-0.00560.00190.00940.00290.01220.26679.9493.5438
70.34720.05910.26410.01220.03890.22140.0121-0.0095-0.00880.0028-0.0029-0.00170.0168-0.0094-0.00920.02880.0004-0.00160.00420.00080.0046-5.206417.2473-5.8296
80.0239-0.044-0.02920.2051-0.04240.11330.0032-0.0014-0.0007-0.01770.00390.0111-0.0068-0.0012-0.00710.02980.0014-0.00390.00390.00190.0032-10.898318.8168-24.342
90.33660.26870.0340.27330.08470.0613-0.0052-0.00760.0123-0.0145-0.0030.0151-0.00510.00160.00820.0284-0.0004-0.00270.001500.005-0.722613.461-18.7117
100.0713-0.10640.02020.20590.00010.0316-0.0060.0010.00170.00050.0041-0.00150.00570.00310.00180.0299-0.0008-0.00050.002200.00243.37557.8198-23.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 9
2X-RAY DIFFRACTION2A10 - 25
3X-RAY DIFFRACTION3A26 - 41
4X-RAY DIFFRACTION4A42 - 51
5X-RAY DIFFRACTION5A52 - 72
6X-RAY DIFFRACTION6A73 - 80
7X-RAY DIFFRACTION7A81 - 102
8X-RAY DIFFRACTION8A103 - 125
9X-RAY DIFFRACTION9A126 - 149
10X-RAY DIFFRACTION10A150 - 189

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