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- PDB-5m2p: The Structure of the Ycf54 protein from Synechocystis sp. PCC6803 -

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Basic information

Entry
Database: PDB / ID: 5m2p
TitleThe Structure of the Ycf54 protein from Synechocystis sp. PCC6803
ComponentsYcf54-like protein
KeywordsPHOTOSYNTHESIS / Mg protoporphyrin IX monomethylester cyclase component. Ycf54 domain PFAM
Function / homologyUncharacterised protein family Ycf54 / Ycf54 protein / Ycf54-like superfamily / Ycf54 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Ycf54-like protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsBaker, P.J. / Bliss, S. / Hollinshead, S. / Hunter, C.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/D526810/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/F016832/1 United Kingdom
CitationJournal: Biochem. J. / Year: 2017
Title: Conserved residues in Ycf54 are required for protochlorophyllide formation in Synechocystis sp. PCC 6803.
Authors: Hollingshead, S. / Bliss, S. / Baker, P.J. / Neil Hunter, C.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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: Ycf54-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5752
Polymers12,4791
Non-polymers961
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.730, 45.930, 119.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-356-

HOH

31A-405-

HOH

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Components

#1: Protein Ycf54-like protein


Mass: 12479.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P72777
#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.: 122 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium fluoride, 2.4M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.33→59.65 Å / Num. obs: 27322 / % possible obs: 99.5 % / Redundancy: 4.5 % / Net I/σ(I): 16.5
Reflection shellRedundancy: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 5703 / Num. unique all: 1916 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HZE

3hze


Resolution: 1.33→59.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.525 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17147 1368 5 %RANDOM
Rwork0.14925 ---
obs0.15034 25912 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.33→59.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 5 122 990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02925
X-RAY DIFFRACTIONr_bond_other_d0.0010.02881
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9891262
X-RAY DIFFRACTIONr_angle_other_deg0.78332047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5742546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.19155
X-RAY DIFFRACTIONr_chiral_restr0.090.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02200
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.93631806
X-RAY DIFFRACTIONr_sphericity_free28.206540
X-RAY DIFFRACTIONr_sphericity_bonded12.52151863
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 104 -
Rwork0.287 1811 -
obs--94.71 %

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