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- PDB-5ze8: Crystal structure of a penta-heme cytochrome c552 from Thermochro... -

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Basic information

Entry
Database: PDB / ID: 5ze8
TitleCrystal structure of a penta-heme cytochrome c552 from Thermochromatium tepidum
Componentscytochrome c552
KeywordsPHOTOSYNTHESIS / cytochrome c / multiheme / purple sulfur bacteria
Function / homologyCytochrome c-552/4 / Cytochrome c554 and c-prime / : / : / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / metal ion binding / HEME C / Cytochrome c552
Function and homology information
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsYu, L.-J. / Chen, J.-H. / Shen, J.-R.
CitationJournal: Photosyn. Res. / Year: 2019
Title: Properties and structure of a low-potential, penta-heme cytochrome c552from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum.
Authors: Chen, J.H. / Yu, L.J. / Boussac, A. / Wang-Otomo, Z.Y. / Kuang, T. / Shen, J.R.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9298
Polymers47,6481
Non-polymers3,2817
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-131 kcal/mol
Surface area18190 Å2
Unit cell
Length a, b, c (Å)144.700, 39.100, 68.650
Angle α, β, γ (deg.)90.000, 109.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cytochrome c552


Mass: 47647.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A0A2P1N6U9*PLUS
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, calcium chloride, ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→68.28 Å / Num. obs: 48283 / % possible obs: 99.94 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/av σ(I): 25.02 / Net I/σ(I): 25.02
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 5.16 / Num. unique obs: 4756 / CC1/2: 0.841 / % possible all: 99.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→68.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.536 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 2437 5 %RANDOM
Rwork0.1577 ---
obs0.1595 45846 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.55 Å2 / Biso mean: 20.417 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→68.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 226 351 3552
Biso mean--13.9 31.77 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193340
X-RAY DIFFRACTIONr_bond_other_d0.0030.022949
X-RAY DIFFRACTIONr_angle_refined_deg2.2612.064585
X-RAY DIFFRACTIONr_angle_other_deg1.2923.0036834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05924.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6261517
X-RAY DIFFRACTIONr_chiral_restr0.1650.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213757
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02689
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 171 -
Rwork0.225 3382 -
all-3553 -
obs--99.52 %

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