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- PDB-3pmq: Crystal structure of the outer membrane decaheme cytochrome MtrF -

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Basic information

Entry
Database: PDB / ID: 3pmq
TitleCrystal structure of the outer membrane decaheme cytochrome MtrF
ComponentsDecaheme cytochrome c MtrF
KeywordsELECTRON TRANSPORT / greek key / c type cytochrome / outer membrane
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #180 / : / Decaheme cytochrome c component MtrF-like domain III / : / Decaheme cytochrome c component MtrC/MtrF N-terminal domain / Decahaem cytochrome, c-type, OmcA/MtrC / : / Outer membrane cytochrome MtrC/MtrF-like, domains II/IV / : / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #180 / : / Decaheme cytochrome c component MtrF-like domain III / : / Decaheme cytochrome c component MtrC/MtrF N-terminal domain / Decahaem cytochrome, c-type, OmcA/MtrC / : / Outer membrane cytochrome MtrC/MtrF-like, domains II/IV / : / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Extracellular respiratory system surface decaheme cytochrome c component MtrF
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsClarke, T.A. / Edwards, M.J. / Richardson, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of a bacterial cell surface decaheme electron conduit.
Authors: Clarke, T.A. / Edwards, M.J. / Gates, A.J. / Hall, A. / White, G.F. / Bradley, J. / Reardon, C.L. / Shi, L. / Beliaev, A.S. / Marshall, M.J. / Wang, Z. / Watmough, N.J. / Fredrickson, J.K. / ...Authors: Clarke, T.A. / Edwards, M.J. / Gates, A.J. / Hall, A. / White, G.F. / Bradley, J. / Reardon, C.L. / Shi, L. / Beliaev, A.S. / Marshall, M.J. / Wang, Z. / Watmough, N.J. / Fredrickson, J.K. / Zachara, J.M. / Butt, J.N. / Richardson, D.J.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decaheme cytochrome c MtrF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,07712
Polymers70,8521
Non-polymers6,22511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)256.640, 256.640, 256.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Decaheme cytochrome c MtrF


Mass: 70852.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shewanella oneidensis (bacteria) / Cellular location: outer membrane / Strain: MR-1 / References: UniProt: Q8EG32
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 9.94 Å3/Da / Density % sol: 87.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM N-(2-Acetamido)iminodiacetate pH 6.5, 15 % ethylene glycol, 1.1 M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 45477 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 94.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6605

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→40 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3212 2296 5.06 %RANDOM
Rwork0.3049 ---
obs0.3057 45357 98 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.365 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 431 0 4826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055027
X-RAY DIFFRACTIONf_angle_d1.1176933
X-RAY DIFFRACTIONf_dihedral_angle_d24.1592816
X-RAY DIFFRACTIONf_chiral_restr0.074695
X-RAY DIFFRACTIONf_plane_restr0.004878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26960.3821220.34212564X-RAY DIFFRACTION94
3.2696-3.34560.41521240.31732585X-RAY DIFFRACTION95
3.3456-3.42930.37271270.32182613X-RAY DIFFRACTION95
3.4293-3.5220.33771410.30372649X-RAY DIFFRACTION97
3.522-3.62560.33061570.29762607X-RAY DIFFRACTION97
3.6256-3.74260.32361480.2922668X-RAY DIFFRACTION98
3.7426-3.87640.28691440.27212700X-RAY DIFFRACTION99
3.8764-4.03150.32791510.27962688X-RAY DIFFRACTION99
4.0315-4.2150.30691490.27992718X-RAY DIFFRACTION99
4.215-4.43710.27541600.27432729X-RAY DIFFRACTION99
4.4371-4.7150.30151510.2762709X-RAY DIFFRACTION99
4.715-5.07880.3271430.28532735X-RAY DIFFRACTION99
5.0788-5.58950.31421540.30972736X-RAY DIFFRACTION100
5.5895-6.39740.31291500.31662749X-RAY DIFFRACTION100
6.3974-8.05650.31491470.32162776X-RAY DIFFRACTION100
8.0565-57.39570.34261280.34552835X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 31.1647 Å / Origin y: 87.873 Å / Origin z: -71.6896 Å
111213212223313233
T0.2834 Å20.0162 Å2-0.4673 Å2-0.1413 Å2-0.2084 Å2--0.82 Å2
L0.9646 °20.7596 °20.8273 °2-0.3439 °20.68 °2--2.1272 °2
S-0.5011 Å °0.1736 Å °0.9293 Å °-0.169 Å °-0.3013 Å °0.4421 Å °-0.5085 Å °-0.0986 Å °0.8058 Å °
Refinement TLS groupSelection details: all

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