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

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Basic information

Entry
Database: PDB / ID: 5mjw
TitleStructure of Psb29 at 1.55A
ComponentsProtein Thf1
KeywordsPHOTOSYNTHESIS / photosystem II FtsH
Function / homologyProtein Thf1 / Thylakoid formation protein / photosystem II assembly / Protein Thf1
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 2, 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


Theoretical massNumber of molelcules
Total (without water)27,2691
Polymers27,2691
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.850, 86.610, 116.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 (strain BP-1) (bacteria)
Strain: BP-1 / Gene: thf1, tlr1134 / Plasmid: pRSETa modified / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q8DJT8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M sodium malonate, pH 7, 20% w/v/ PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.47→55.26 Å / Num. obs: 11662 / % possible obs: 99.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.34 % / Rmerge(I) obs: 0.062 / Net I/av σ(I): 16.5176 / Net I/σ(I): 6.2893
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 6.45 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.67 / % possible all: 98.77

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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: 2.47→55.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 18.463 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.237 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 555 4.8 %RANDOM
Rwork0.2176 ---
obs0.21913 11106 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0 Å2
2--2.42 Å20 Å2
3----2.72 Å2
Refinement stepCycle: 1 / Resolution: 2.47→55.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 0 7 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191613
X-RAY DIFFRACTIONr_bond_other_d0.0010.021490
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9612186
X-RAY DIFFRACTIONr_angle_other_deg0.93233451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09823.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4451514
X-RAY DIFFRACTIONr_chiral_restr0.070.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
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_it1.0114.413779
X-RAY DIFFRACTIONr_mcbond_other1.0114.41778
X-RAY DIFFRACTIONr_mcangle_it1.6876.617972
X-RAY DIFFRACTIONr_mcangle_other1.6876.62973
X-RAY DIFFRACTIONr_scbond_it0.9254.521834
X-RAY DIFFRACTIONr_scbond_other0.9254.516832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5956.7411214
X-RAY DIFFRACTIONr_long_range_B_refined2.96351.5581765
X-RAY DIFFRACTIONr_long_range_B_other2.96251.5821766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 39 -
Rwork0.267 795 -
obs--98.7 %
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)
18.2691-1.8498-7.6896.48354.421321.76350.1928-0.00690.1562-0.2481-0.09940.0811-0.21220.0698-0.09340.2287-0.0370.01570.01390.00830.05452.411-5.38311.205
25.8025-0.2893.7863.5677-1.293725.6877-0.0160.2081-0.15270.0020.0543-0.01330.25790.1227-0.03830.21660.01750.01140.0203-0.03170.0751-2.036-14.844-17.117
33.0190.51172.79173.54232.750410.60850.1102-0.3241-0.21180.6980.00840.41460.6925-0.5492-0.11860.3631-0.03290.07440.2886-0.00410.1199-12.076-19.273-12.433
48.53233.36134.92666.97491.68575.74760.34210.06220.18590.3784-0.35080.664-0.252-0.88270.00860.33880.18870.10820.41960.00370.1893-13.286-10.186-13.433
57.04962.42586.30747.25492.03716.53530.5771-0.793-0.58850.15260.10750.25280.5215-0.5941-0.68450.139-0.1306-0.10280.28420.08010.2731-22.397-26.974-27.87
613.6814.45992.06949.9112-1.17644.48770.4305-0.5924-0.2061-0.04650.03150.17860.5445-0.3862-0.4620.2475-0.0385-0.10460.1941-0.01160.0772-11.841-27.49-23.802
771.67678.4461-25.41589.7245-11.661817.626-0.65340.0193-0.5609-0.09780.54320.01890.2555-0.45140.11021.2718-0.1509-0.27661.03350.07060.9501-11.18-41.09-22.21
89.46030.99964.31448.2147-0.21879.17270.55310.9417-1.1387-0.83490.4254-0.23981.0495-0.1541-0.97850.6253-0.0614-0.18560.2239-0.12560.2935-9.625-33.788-32.225
95.8504-4.23716.92893.0925-5.455134.67580.7409-0.2377-0.3782-0.51440.14910.16771.34890.9362-0.890.51390.0022-0.08680.1841-0.05680.9371-2.747-31.87-20.8
106.7048-6.1407-5.874814.125114.052250.356-0.5283-0.0338-0.00930.38330.08880.7213-0.2656-1.18160.43950.35750.0404-0.11560.35880.01220.3449-4.808-30.1840.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 22
2X-RAY DIFFRACTION2A23 - 47
3X-RAY DIFFRACTION3A48 - 72
4X-RAY DIFFRACTION4A73 - 90
5X-RAY DIFFRACTION5A91 - 126
6X-RAY DIFFRACTION6A127 - 149
7X-RAY DIFFRACTION7A150 - 156
8X-RAY DIFFRACTION8A157 - 170
9X-RAY DIFFRACTION9A171 - 182
10X-RAY DIFFRACTION10A183 - 198

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