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- PDB-5m2r: The Structure of the Ycf54 A9G mutant protein from Synechocystis ... -

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Basic information

Entry
Database: PDB / ID: 5m2r
TitleThe Structure of the Ycf54 A9G mutant 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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBaker, P.J. / Bliss, S. / Hollinshead, S. / Hunter, 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)12,5612
Polymers12,4651
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.200, 46.130, 119.660
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-335-

HOH

31A-342-

HOH

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Components

#1: Protein Ycf54-like protein


Mass: 12465.073 Da / Num. of mol.: 1 / Mutation: A9G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / 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.: 84 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1M trisodium citrate, 2.4M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→24.54 Å / Num. obs: 18771 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8496 / Rpim(I) all: 0.35 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M2P

5m2p


Resolution: 1.5→24.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.964 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24331 960 5.1 %RANDOM
Rwork0.18204 ---
obs0.18503 17771 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.938 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---0.05 Å20 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 1.5→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 5 84 951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02907
X-RAY DIFFRACTIONr_bond_other_d0.0010.02853
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9871234
X-RAY DIFFRACTIONr_angle_other_deg0.77931979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8675109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55725.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.153154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
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_restr3.2931760
X-RAY DIFFRACTIONr_sphericity_free26.59537
X-RAY DIFFRACTIONr_sphericity_bonded12.69651785
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 75 -
Rwork0.246 1249 -
obs--97.5 %

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