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- PDB-6cuk: Engineered Cytochrome c from Rhodothermus marinus, Rma TDE -

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Basic information

Entry
Database: PDB / ID: 6cuk
TitleEngineered Cytochrome c from Rhodothermus marinus, Rma TDE
ComponentsCytochrome c
KeywordsLYASE / Carbene transferase / silicon-carbon bond
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLewis, R.D. / Buller, A.R. / Arnold, F.H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1513007 United States
National Science Foundation (NSF, United States)CHE-1361104 United States
National Science Foundation (NSF, United States)CBET-1403077 United States
Caltech Innovation Initiative United States
Jacobs Institute for Molecular Medicine United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Catalytic iron-carbene intermediate revealed in a cytochromeccarbene transferase.
Authors: Lewis, R.D. / Garcia-Borras, M. / Chalkley, M.J. / Buller, A.R. / Houk, K.N. / Kan, S.B.J. / Arnold, F.H.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 / _citation_author.name
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 10, 2021Group: 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
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.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
Revision 2.1Oct 4, 2023Group: 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: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6482
Polymers14,0301
Non-polymers6191
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-25 kcal/mol
Surface area6120 Å2
Unit cell
Length a, b, c (Å)60.038, 60.038, 77.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome c


Mass: 14029.785 Da / Num. of mol.: 1 / Mutation: V75T, M100D, M103E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: cytC / Production host: Escherichia coli (E. coli) / References: UniProt: B3FQS5
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.87 Å3/Da / Density % sol: 57.09 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.43-1.48 M (NH4)2SO4 300-400 mM NaSCN 1.5% isopropanol 14.0 mg/mL protein in 20 mM Tris pH 7.5 2:1 protein to well solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.47→38.65 Å / Num. obs: 27920 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 15.2
Reflection shellResolution: 1.47→1.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP5

3cp5


Resolution: 1.47→38.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.813 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20856 1280 4.6 %RANDOM
Rwork0.18384 ---
obs0.18497 26618 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.47→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 43 84 1012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021022
X-RAY DIFFRACTIONr_bond_other_d0.0020.02923
X-RAY DIFFRACTIONr_angle_refined_deg1.7192.11403
X-RAY DIFFRACTIONr_angle_other_deg1.033.0022131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31724.69449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33815169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.991159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211177
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02189
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_it0.7781.16494
X-RAY DIFFRACTIONr_mcbond_other0.7691.157493
X-RAY DIFFRACTIONr_mcangle_it1.2821.738628
X-RAY DIFFRACTIONr_mcangle_other1.2831.741629
X-RAY DIFFRACTIONr_scbond_it1.0321.278527
X-RAY DIFFRACTIONr_scbond_other1.0311.279528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4291.893776
X-RAY DIFFRACTIONr_long_range_B_refined4.24614.2061151
X-RAY DIFFRACTIONr_long_range_B_other4.11813.8581140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 95 -
Rwork0.231 1917 -
obs--98.82 %
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)
16.87732.8839-5.108610.1562.23375.957-0.13720.16380.0402-0.61990.3771-0.4014-0.12640.1116-0.23990.1550.13070.01220.3565-0.03720.073613.194379.05781.1902
22.36620.8753-1.346210.0856-1.73965.59760.1358-0.11690.04720.0561-0.0805-0.5191-0.09240.2942-0.05540.0183-0.0233-0.01680.1125-0.01690.092511.688780.046889.3049
34.01092.0873-1.59374.80312.17876.5769-0.65920.479-0.5878-0.21590.3257-0.99870.26070.36670.33350.1661-0.02990.06120.20250.01830.34097.544362.478792.3364
410.5105-3.8372.02153.8211-0.55894.75870.0189-0.0564-0.44870.0533-0.0040.26920.36-0.2482-0.01490.0948-0.0291-0.00610.07570.00810.0392-3.466463.030496.2371
55.4929-2.98660.81324.42180.71437.440.0926-0.115-0.03230.0498-0.0020.18350.0165-0.3591-0.09060.0125-0.0118-0.00170.0940.00730.0448-9.042270.550392.7779
61.9196-0.3197-1.57421.95342.19183.4589-0.03540.28970.00860.0764-0.16330.12510.1161-0.3720.19870.013700.00680.13950.00640.0449-10.095472.29182.4057
72.7114-3.279-0.30479.51777.49179.1772-0.02740.0501-0.0683-0.2027-0.18770.2572-0.2937-0.18060.21510.03980.0343-0.01870.19480.0370.0868-11.332574.646875.66
81.97640.94030.37861.0960.43542.5853-0.02140.18820.0557-0.00130.062-0.039-0.08230.0172-0.04060.01390.0009-0.00620.10330.02090.03122.015974.887283.3118
97.8351-4.1173-4.45745.35121.517211.2137-0.11540.23810.81360.05740.2615-0.5439-1.18070.0062-0.14620.1855-0.0397-0.05420.08880.04810.12945.831986.713180.7329
107.7941-1.1588-3.65627.2557-6.88159.53020.0820.28530.9816-0.19110.3712-0.1820.1646-0.5061-0.45320.1263-0.1038-0.0370.29340.01220.16282.677382.515675.1154
1112.81314.03675.787617.18093.74976.4224-0.28920.168-0.0244-0.4570.3274-0.1139-0.0156-0.2418-0.03820.1704-0.00150.14780.29430.20150.2712-4.023283.696873.3038
122.7755-0.77983.83873.4975-9.96831.2904-0.00690.0730.21630.0680.2165-0.0107-0.6112-0.1363-0.20960.1761-0.0210.0680.2331-0.00020.1936-6.852984.615686.7181
136.4113-3.85450.8778.174-0.27066.03330.14360.2230.26690.0594-0.12030.1234-0.3124-0.1327-0.02330.0805-0.01790.00190.0640.0060.03930.773577.787697.1221
140.44521.50320.28896.31222.07464.42370.08180.0318-0.01380.0839-0.0476-0.09320.0953-0.0412-0.03420.06610.0139-0.00070.080.00050.0407-0.346369.597891.785
156.3423-2.15150.0023.7924-0.898512.23210.12170.4797-0.9575-0.34150.0519-0.17511.3589-0.0311-0.17360.1681-0.0027-0.00210.0755-0.10320.2358-0.069661.489585.6684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 13
2X-RAY DIFFRACTION2A14 - 23
3X-RAY DIFFRACTION3A24 - 30
4X-RAY DIFFRACTION4A31 - 35
5X-RAY DIFFRACTION5A36 - 44
6X-RAY DIFFRACTION6A45 - 52
7X-RAY DIFFRACTION7A53 - 56
8X-RAY DIFFRACTION8A57 - 81
9X-RAY DIFFRACTION9A82 - 87
10X-RAY DIFFRACTION10A88 - 92
11X-RAY DIFFRACTION11A93 - 97
12X-RAY DIFFRACTION12A98 - 103
13X-RAY DIFFRACTION13A104 - 108
14X-RAY DIFFRACTION14A109 - 117
15X-RAY DIFFRACTION15A118 - 123

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