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

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Basic information

Entry
Database: PDB / ID: 5mjr
TitleStructure of Psb29 at 1.55A
ComponentsProtein Thf1
KeywordsPHOTOSYNTHESIS / photosystem II FtsH
Function / homologyProtein Thf1 / Thylakoid formation protein / protein import into chloroplast thylakoid membrane / protein import into chloroplast stroma / plasma membrane-derived thylakoid photosystem II / thylakoid membrane organization / photosystem II assembly / Protein Thf1
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsMurray, J.W. / Kozlo, A.
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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3652
Polymers27,2691
Non-polymers961
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-11 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.660, 56.100, 44.550
Angle α, β, γ (deg.)90.00, 105.70, 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): KRZ / References: UniProt: Q8DJT8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M trisodium citrate, 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: 1.38→42.89 Å / Num. obs: 37960 / % possible obs: 98.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.56 % / Rmerge(I) obs: 0.113 / Net I/av σ(I): 17.5351 / Net I/σ(I): 5.1923
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 0.34 / % possible all: 98.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MJO

5mjo


Resolution: 1.38→42.89 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.629 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15544 1895 5 %RANDOM
Rwork0.11356 ---
obs0.11571 36039 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.71 Å2
2---0.18 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.38→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 5 240 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191587
X-RAY DIFFRACTIONr_bond_other_d0.0020.021454
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.9592160
X-RAY DIFFRACTIONr_angle_other_deg1.1633373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4485196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41623.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011514
X-RAY DIFFRACTIONr_chiral_restr0.1660.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02332
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_it2.2471.339766
X-RAY DIFFRACTIONr_mcbond_other2.2481.336765
X-RAY DIFFRACTIONr_mcangle_it2.5532.019962
X-RAY DIFFRACTIONr_mcangle_other2.5522.022963
X-RAY DIFFRACTIONr_scbond_it5.2371.809821
X-RAY DIFFRACTIONr_scbond_other5.2391.804817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8852.5551190
X-RAY DIFFRACTIONr_long_range_B_refined4.68418.361898
X-RAY DIFFRACTIONr_long_range_B_other4.41317.451838
X-RAY DIFFRACTIONr_rigid_bond_restr5.18733041
X-RAY DIFFRACTIONr_sphericity_free32.7865150
X-RAY DIFFRACTIONr_sphericity_bonded14.53953092
LS refinement shellResolution: 1.384→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 144 -
Rwork0.149 2630 -
obs--98.4 %

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