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- PDB-5oj3: YCF48 from Cyanidioschyzon merolae -

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Basic information

Entry
Database: PDB / ID: 5oj3
TitleYCF48 from Cyanidioschyzon merolae
ComponentsPhotosystem II stability/assembly factor HCF136
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II
Function / homologyPhotosynthesis system II assembly factor Ycf48/Hcf136-like domain / Photosynthesis system II assembly factor YCF48 / WD40/YVTN repeat-like-containing domain superfamily / Photosystem II stability/assembly factor HCF136
Function and homology information
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.982 Å
AuthorsMichoux, F. / Murray, J.W. / Nixon, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L003260/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ycf48 involved in the biogenesis of the oxygen-evolving photosystem II complex is a seven-bladed beta-propeller protein.
Authors: Yu, J. / Knoppova, J. / Michoux, F. / Bialek, W. / Cota, E. / Shukla, M.K. / Straskova, A. / Pascual Aznar, G. / Sobotka, R. / Komenda, J. / Murray, J.W. / Nixon, P.J.
History
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Photosystem II stability/assembly factor HCF136
B: Photosystem II stability/assembly factor HCF136


Theoretical massNumber of molelcules
Total (without water)95,1252
Polymers95,1252
Non-polymers00
Water00
1
A: Photosystem II stability/assembly factor HCF136


Theoretical massNumber of molelcules
Total (without water)47,5621
Polymers47,5621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Photosystem II stability/assembly factor HCF136


Theoretical massNumber of molelcules
Total (without water)47,5621
Polymers47,5621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.810, 97.120, 110.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Photosystem II stability/assembly factor HCF136


Mass: 47562.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Gene: CYME_CMO314C / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Variant (production host): KRX / References: UniProt: M1VJU3

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10 % w/v PEG 1000/ 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.12713 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.98→37.69 Å / Num. obs: 13864 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.128 / Rsym value: 0.074 / Net I/σ(I): 10.6
Reflection shellResolution: 2.98→3.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 688 / CC1/2: 0.537 / Rpim(I) all: 0.542 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XBG

2xbg


Resolution: 2.982→37.69 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 640 4.63 %Random
Rwork0.223 ---
obs0.2255 13818 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.982→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 0 0 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045067
X-RAY DIFFRACTIONf_angle_d0.9426891
X-RAY DIFFRACTIONf_dihedral_angle_d5.7582914
X-RAY DIFFRACTIONf_chiral_restr0.054747
X-RAY DIFFRACTIONf_plane_restr0.005892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9818-3.21190.39561190.30882594X-RAY DIFFRACTION100
3.2119-3.53490.33961340.27112581X-RAY DIFFRACTION99
3.5349-4.04590.26121340.23362576X-RAY DIFFRACTION98
4.0459-5.09540.28681230.18432664X-RAY DIFFRACTION100
5.0954-37.70990.2351300.20552763X-RAY DIFFRACTION100
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)
11.0341-0.71050.11914.0111-2.53273.59360.08270.6765-0.1347-0.6692-0.468-0.48520.46310.70840.28210.58590.14140.16020.79210.05870.4665.1069-9.9404-14.8621
24.42661.4078-3.02471.3973-0.35032.8219-0.18451.7943-1.1468-0.7017-0.1476-0.46561.1658-0.1880.63720.7360.33320.1360.8254-0.18170.7591-0.304-22.9882-8.8544
32.72271.40011.05182.8135-0.09872.15850.22390.131-0.07710.6188-0.4182-0.32990.74910.09710.01220.62540.06160.01390.3411-0.08830.381-4.6063-17.9293-1.1107
44.4362-0.30130.69737.2146-2.27154.929-0.20580.2093-0.1051-0.30270.06470.4489-0.2041-0.52640.08610.40410.06060.02620.4267-0.07790.2601-18.2312-5.2735-2.0656
53.99080.5608-0.3723.9908-1.66884.8776-0.01250.32390.8180.02720.0570.0453-0.592-0.3098-0.13920.45440.1013-0.02840.38710.09430.4229-11.25539.6385-6.8804
65.0575-1.026-2.32358.40122.79763.7285-0.10020.57330.4188-0.2621-0.2827-0.5822-0.19790.91450.45090.47510.03390.11970.66870.26930.48540.04925.9978-17.2116
72.7545-0.64470.59936.28851.15042.8339-0.2408-0.36560.20110.56080.06650.0475-0.0444-0.15970.24990.46880.0576-0.00530.5153-0.12050.3262-4.2439-3.480427.1244
85.55682.3338-3.01354.0242-0.40517.2614-0.5356-0.074-1.5072-0.181-0.1775-0.45390.82481.23370.27280.6509-0.0025-0.11020.56810.20460.68281.6703-16.504825.1193
95.84842.29520.9614.90481.72022.46-0.24790.3702-0.34650.24030.14850.1640.63770.6185-0.03060.45390.06710.05040.4363-0.01670.32025.9838-14.359316.015
107.3631-0.59141.10767.0718-0.28912.845-0.1514-0.00480.3183-0.2468-0.1211-0.9565-0.03530.42450.16490.3229-0.01760.0260.4680.02610.469317.496-1.330512.4
115.3443-0.7030.28724.03260.21313.8858-0.07540.0541.0385-0.2952-0.1292-0.2636-0.90330.20960.20860.5288-0.1254-0.09990.38930.07140.762910.441413.96811.1189
122.7087-0.6474-2.26715.0024-3.00044.4427-0.2593-0.59670.35360.6478-0.0453-0.4072-0.7091-0.23850.35530.63310.0559-0.20270.4292-0.19630.6048-1.067413.424721.9472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 107:192
2X-RAY DIFFRACTION2chain A and resid 193:211
3X-RAY DIFFRACTION3chain A and resid 212:241
4X-RAY DIFFRACTION4chain A and resid 242:337
5X-RAY DIFFRACTION5chain A and resid 338:395
6X-RAY DIFFRACTION6chain A and resid 396:435
7X-RAY DIFFRACTION7chain B and resid 107:192
8X-RAY DIFFRACTION8chain B and resid 193:211
9X-RAY DIFFRACTION9chain B and resid 212:241
10X-RAY DIFFRACTION10chain B and resid 242:337
11X-RAY DIFFRACTION11chain B and resid 338:395
12X-RAY DIFFRACTION12chain B and resid 396:435

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