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- PDB-6onq: Crystal structure of c-type cytochrome XoxG from Methylobacterium... -

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Basic information

Entry
Database: PDB / ID: 6onq
TitleCrystal structure of c-type cytochrome XoxG from Methylobacterium extorquens AM1
ComponentsCytochrome c XoxG
KeywordsELECTRON TRANSPORT / Cytochrome / heme / methanol oxidation / lanthanide
Function / homologyC-type cytochrome, methanol metabolism-related / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome c-like domain superfamily / electron transfer activity / heme binding / metal ion binding / HEME C / Cytochrome c
Function and homology information
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsMcBride, M.J. / Featherston, E.R. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chembiochem / Year: 2019
Title: Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity.
Authors: Featherston, E.R. / Rose, H.R. / McBride, M.J. / Taylor, E.M. / Boal, A.K. / Cotruvo Jr., J.A.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
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_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _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 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.dist / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Cytochrome c XoxG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9552
Polymers21,3361
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.841, 95.841, 80.411
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Cytochrome c XoxG


Mass: 21336.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: maxG' / Production host: Escherichia coli (E. coli) / References: UniProt: P71510
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: .2 M sodium acetate, 0.1 M phosphate-citra te pH 4.2, and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.6984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6984 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 6337 / % possible obs: 98.6 % / Redundancy: 37.7 % / Biso Wilson estimate: 39.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.02 / Net I/σ(I): 39
Reflection shellResolution: 2.71→2.76 Å / Rmerge(I) obs: 1.242 / Num. unique obs: 305 / CC1/2: 0.898 / Rpim(I) all: 0.256

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
REFMAC1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.71→41.5 Å / SU ML: 0.3258 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.3881
RfactorNum. reflection% reflection
Rfree0.2484 313 5.02 %
Rwork0.1937 --
obs0.1963 6236 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.79 Å2
Refinement stepCycle: LAST / Resolution: 2.71→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 43 0 1295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731336
X-RAY DIFFRACTIONf_angle_d0.96951812
X-RAY DIFFRACTIONf_chiral_restr0.0465171
X-RAY DIFFRACTIONf_plane_restr0.0046235
X-RAY DIFFRACTIONf_dihedral_angle_d8.4804778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-3.410.31611520.2332857X-RAY DIFFRACTION98.08
3.41-41.510.21631610.17583066X-RAY DIFFRACTION99.38

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