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- PDB-5m2u: The Structure of the Ycf54 protein from Synechocystis sp. PCC6803 -

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Basic information

Entry
Database: PDB / ID: 5m2u
TitleThe Structure of the Ycf54 protein from Synechocystis sp. PCC6803
ComponentsYcf54
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: 2.2 Å
AuthorsBaker, P.J. / Bliss, S. / Hollingshead, 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

Downloads & links

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Assembly

Deposited unit
A: Ycf54
B: Ycf54
C: Ycf54
D: Ycf54


Theoretical massNumber of molelcules
Total (without water)49,5724
Polymers49,5724
Non-polymers00
Water2,828157
1
A: Ycf54


Theoretical massNumber of molelcules
Total (without water)12,3931
Polymers12,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ycf54


Theoretical massNumber of molelcules
Total (without water)12,3931
Polymers12,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ycf54


Theoretical massNumber of molelcules
Total (without water)12,3931
Polymers12,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ycf54


Theoretical massNumber of molelcules
Total (without water)12,3931
Polymers12,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.520, 91.150, 120.300
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
Ycf54


Mass: 12392.982 Da / Num. of mol.: 4 / Mutation: R82A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2.2M 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 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→27.8 Å / Num. obs: 31240 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Net I/σ(I): 22.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2237 / Rpim(I) all: 0.35 / % possible all: 98.5

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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: 2.2→27.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.922 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24958 1573 5 %RANDOM
Rwork0.20555 ---
obs0.20775 29636 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.305 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---0.82 Å20 Å2
3----2.8 Å2
Refinement stepCycle: 1 / Resolution: 2.2→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 157 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023522
X-RAY DIFFRACTIONr_bond_other_d0.0010.023347
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9764784
X-RAY DIFFRACTIONr_angle_other_deg0.77337751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64225.412170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8561512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 106 -
Rwork0.292 2116 -
obs--98.19 %

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