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- PDB-6ee7: Small tetraheme cytochrome c from Shewanella oneidensis -

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Basic information

Entry
Database: PDB / ID: 6ee7
TitleSmall tetraheme cytochrome c from Shewanella oneidensis
ComponentsPeriplasmic tetraheme cytochrome c CctA
KeywordsELECTRON TRANSPORT / electron transfer
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Tetrahaem cytochrome domain / Cytochrome c3 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Periplasmic tetraheme cytochrome c CctA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.394 Å
AuthorsHuang, J. / Zarzycki, J. / Ducat, D.C. / Kramer, D.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)135959 United States
Department of Energy (DOE, United States)DE-FG02-91ER20021 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Mesoscopic to Macroscopic Electron Transfer by Hopping in a Crystal Network of Cytochromes.
Authors: Huang, J. / Zarzycki, J. / Gunner, M.R. / Parson, W.W. / Kern, J.F. / Yano, J. / Ducat, D.C. / Kramer, D.M.
History
DepositionAug 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 27, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / 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 / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_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
Revision 2.1Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.ptnr2_symmetry / _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_asym_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.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic tetraheme cytochrome c CctA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3448
Polymers9,6741
Non-polymers2,6707
Water2,522140
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)24.595, 63.856, 28.979
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic tetraheme cytochrome c CctA


Mass: 9673.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: cctA, SO_2727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EDL6
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.21 Å3/Da / Density % sol: 44 % / Description: elongated plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5 mg/mL of purified cytochrome (1 mM HEPES pH 8.0) were mixed with reservoir solution (16 PEG 3350, 15 mM ZnSO4 in 1:1 (v/v) ratio and placed at 277 K in sitting drop vapor diffusion dishes. ...Details: 5 mg/mL of purified cytochrome (1 mM HEPES pH 8.0) were mixed with reservoir solution (16 PEG 3350, 15 mM ZnSO4 in 1:1 (v/v) ratio and placed at 277 K in sitting drop vapor diffusion dishes. Crystals were harvested after ca. 10 days and transferred to 30% PEG 400 before freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.394→16.922 Å / Num. obs: 34487 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.041 / Net I/σ(I): 10.8
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3220 / CC1/2: 0.836 / Rpim(I) all: 0.31 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1R

1m1r


Resolution: 1.394→16.922 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 19.14
RfactorNum. reflection% reflection
Rfree0.1832 3428 9.99 %
Rwork0.1639 --
obs0.1658 34325 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.394→16.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms669 0 175 140 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024884
X-RAY DIFFRACTIONf_angle_d1.6981248
X-RAY DIFFRACTIONf_dihedral_angle_d28.157278
X-RAY DIFFRACTIONf_chiral_restr0.08996
X-RAY DIFFRACTIONf_plane_restr0.009151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3936-1.41350.36891140.33321009X-RAY DIFFRACTION78
1.4135-1.43460.31711500.29691338X-RAY DIFFRACTION100
1.4346-1.4570.24611460.27231321X-RAY DIFFRACTION100
1.457-1.48090.2611370.24411253X-RAY DIFFRACTION100
1.4809-1.50640.24631440.23081295X-RAY DIFFRACTION100
1.5064-1.53380.18741490.22471354X-RAY DIFFRACTION100
1.5338-1.56330.21481410.21231246X-RAY DIFFRACTION100
1.5633-1.59520.25271530.19681352X-RAY DIFFRACTION99
1.5952-1.62980.20111410.19851324X-RAY DIFFRACTION99
1.6298-1.66770.22171400.18161265X-RAY DIFFRACTION99
1.6677-1.70940.17711460.18271300X-RAY DIFFRACTION99
1.7094-1.75550.23331430.16891322X-RAY DIFFRACTION99
1.7555-1.80710.191420.17141267X-RAY DIFFRACTION99
1.8071-1.86540.1921440.16081294X-RAY DIFFRACTION99
1.8654-1.9320.15811430.14371312X-RAY DIFFRACTION99
1.932-2.00920.16641430.14921268X-RAY DIFFRACTION98
2.0092-2.10050.19321450.14251296X-RAY DIFFRACTION99
2.1005-2.2110.18531460.13891320X-RAY DIFFRACTION100
2.211-2.34920.15121450.14861281X-RAY DIFFRACTION99
2.3492-2.530.1671480.15711309X-RAY DIFFRACTION100
2.53-2.78360.1691430.14861299X-RAY DIFFRACTION99
2.7836-3.18410.13971400.14681306X-RAY DIFFRACTION99
3.1841-4.00280.15381450.13261309X-RAY DIFFRACTION100
4.0028-16.9230.1831400.15541257X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.60830.0047-0.60822.9469-0.47883.48460.0323-0.0654-0.21210.2703-0.02150.06380.3279-0.1334-0.01710.1365-0.0103-0.0010.09990.00310.1687-22.6422-11.26528.2577
23.20192.3481.17642.75120.75390.9359-0.06250.0908-0.1292-0.17540.0362-0.16360.05430.08080.00710.11430.01040.00490.1201-0.00520.125-11.8768-5.97419.7875
31.4609-0.3173-0.73660.82580.6291.08680.03060.09150.0866-0.11740.0092-0.0107-0.1391-0.0451-0.02650.12130.007-0.01160.11720.01610.1109-20.76124.945122.7451
43.3434-0.427-1.24741.90880.58851.50150.08020.13330.2438-0.04340.0002-0.0741-0.1466-0.0348-0.06060.13890.00040.00360.12120.02320.1202-19.621311.541331.0911
51.36730.0437-0.67782.10370.19471.3394-0.0107-0.0455-0.16980.2108-0.0716-0.07080.19350.08570.06490.14680.0052-0.00210.1229-0.00060.1236-18.0933-3.169133.5197
64.26933.93630.95388.22182.45723.8242-0.121-0.057-0.17370.0813-0.01490.07550.1655-0.05050.11690.1989-0.00890.01740.17180.01910.1587-21.95461.130940.2139
72.7724-0.9553-0.97211.4337-0.42441.8391-0.0163-0.29790.02170.17770.0747-0.16160.08780.0862-0.05110.1882-0.0068-0.02410.1641-0.00580.1445-16.988610.330844.3416
84.913-0.1880.35085.16250.27835.7590.10410.04160.28340.00340.08670.1871-0.2335-0.2898-0.18010.18860.03340.00550.2013-0.01110.1579-29.574210.837341.6406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 70 )
6X-RAY DIFFRACTION6chain 'A' and (resid 71 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 84 )
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 90 )

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