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- PDB-2xbg: Crystal Structure of YCF48 from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 2xbg
TitleCrystal Structure of YCF48 from Thermosynechococcus elongatus
ComponentsYCF48-LIKE PROTEIN
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II / BETA-PROPELLER / ASSEMBLY FACTOR
Function / homologyPhotosynthesis system II assembly factor Ycf48/Hcf136 / Photosynthesis system II assembly factor Ycf48/Hcf136-like domain / Photosynthesis system II assembly factor YCF48 / plasma membrane-derived thylakoid lumen / photosystem II / photosynthesis / WD40/YVTN repeat-like-containing domain superfamily / Photosystem II assembly protein Ycf48
Function and homology information
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMichoux, F. / Takasaka, K. / Nixon, P. / Murray, J.W.
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
DepositionApr 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YCF48-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,2671
Polymers36,2671
Non-polymers00
Water4,666259
1
A: YCF48-LIKE PROTEIN

A: YCF48-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)72,5332
Polymers72,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1850 Å2
ΔGint-9.8 kcal/mol
Surface area27110 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.726, 75.676, 148.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein YCF48-LIKE PROTEIN


Mass: 36266.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Plasmid: PRSET-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KRX / References: UniProt: Q8DI95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growDetails: 0.1M MAGNESIUM SULFATE, 10% W/V PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→44.87 Å / Num. obs: 50546 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.21 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.44
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.22 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→37.838 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.186 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 2542 5.03 %RANDOM
Rwork0.1609 ---
obs0.164 50511 99.71 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.787 Å2
Baniso -1Baniso -2Baniso -3
1--1.435 Å2-0 Å20 Å2
2--1.273 Å2-0 Å2
3---0.162 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 259 2667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2261.9383468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05423.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0681519
X-RAY DIFFRACTIONr_chiral_restr0.1330.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212891
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2402
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21159
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8751.51556
X-RAY DIFFRACTIONr_mcbond_other1.0821.5638
X-RAY DIFFRACTIONr_mcangle_it4.2322514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7733980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.9674.5948
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.56134256
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 174 -
Rwork0.185 3509 -
obs--99.892 %

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