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- PDB-6rsl: Cytochrome c co-crystallized with 10 eq. sulfonato-calix[8]arene ... -

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Basic information

Entry
Database: PDB / ID: 6rsl
TitleCytochrome c co-crystallized with 10 eq. sulfonato-calix[8]arene and 25 eq. spermine (dry-coating method) - structure III
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / Molecular glues / Molecular switch / spermine / polyamine / calixarene / supramolecular chemistry / cytc
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
sulfonato-calix[8]arene / HEME C / SPERMINE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsEngilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Acs Nano / Year: 2019
Title: Tuning Protein Frameworks via Auxiliary Supramolecular Interactions.
Authors: Engilberge, S. / Rennie, M.L. / Dumont, E. / Crowley, P.B.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,26022
Polymers24,0842
Non-polymers12,17720
Water3,981221
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,13011
Polymers12,0421
Non-polymers6,08810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,13011
Polymers12,0421
Non-polymers6,08810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.036, 105.036, 86.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21B-411-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c iso-1


Mass: 12041.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.96 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.20 M Ammonium sulfate, 0.02 M sulfonato-calix[8]arene, 0.05 M spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 1.988→74.272 Å / Num. obs: 33926 / % possible obs: 100 % / Redundancy: 25.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.344 / Rpim(I) all: 0.072 / Rrim(I) all: 0.351 / Net I/σ(I): 6.4
Reflection shellResolution: 1.988→2.022 Å / Redundancy: 26.7 % / Rmerge(I) obs: 2.169 / Num. unique obs: 1668 / CC1/2: 0.928 / Rpim(I) all: 0.428 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GD9

6gd9


Resolution: 1.988→56.383 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 42.64
RfactorNum. reflection% reflection
Rfree0.2647 1657 4.93 %
Rwork0.2414 --
obs0.2425 33634 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.988→56.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 794 221 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082576
X-RAY DIFFRACTIONf_angle_d1.3923606
X-RAY DIFFRACTIONf_dihedral_angle_d29.064904
X-RAY DIFFRACTIONf_chiral_restr0.048238
X-RAY DIFFRACTIONf_plane_restr0.008358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9876-2.04610.31651290.32052642X-RAY DIFFRACTION100
2.0461-2.11210.28931290.31472656X-RAY DIFFRACTION100
2.1121-2.18760.30941350.30022629X-RAY DIFFRACTION100
2.1876-2.27520.34011420.28632652X-RAY DIFFRACTION100
2.2752-2.37880.35471480.27832605X-RAY DIFFRACTION99
2.3788-2.50420.26261490.26362648X-RAY DIFFRACTION100
2.5042-2.66110.33721170.25922683X-RAY DIFFRACTION100
2.6611-2.86650.28671540.25742654X-RAY DIFFRACTION100
2.8665-3.1550.23961330.25972695X-RAY DIFFRACTION100
3.155-3.61150.28911380.21762692X-RAY DIFFRACTION99
3.6115-4.54970.19731400.1972682X-RAY DIFFRACTION98
4.5497-56.40610.2361430.21512739X-RAY DIFFRACTION95
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)
11.4912.01352.62547.14911.28667.7482-0.619-0.2002-0.31880.8483-0.43341.90460.1698-1.54421.05330.7597-0.74980.0010.72750.08010.722522.2854-15.8968-14.9952
28.49615.8594-1.36789.561-3.4969.32160.0310.9501-1.02210.2782-0.0005-0.1620.4983-0.68090.03060.324-0.12330.06720.5266-0.10210.36733.066-18.2625-26.0241
33.50350.45125.96542.53211.56192.02320.2936-0.1835-0.43450.2840.0215-0.13910.5725-0.0563-0.3020.25610.01350.06390.33420.06540.381442.6029-12.6564-21.4486
43.79480.66861.18653.0273-0.53551.70120.0323-0.05160.13950.3124-0.162-0.50680.01010.64970.09440.1779-0.015-0.05550.3928-0.0120.352941.6468-7.4786-14.5738
55.4057-5.1917-0.62697.34332.69769.1073-0.1534-0.1517-0.11960.95950.1554-1.5807-0.10040.58920.01580.3037-0.0387-0.07140.3616-0.13990.653945.0619-0.445-16.0538
61.79020.3811-1.0644.271-0.25125.2225-0.2540.409-0.05240.31630.00310.06270.1923-0.39420.28770.19870.0063-0.02160.4048-0.13490.362830.5286-1.7073-15.6282
79.46624.9954-2.46316.41742.06153.7277-0.485-0.09940.7038-0.94320.5410.2971-0.4707-0.05750.02890.20760.0576-0.09760.320.08740.388831.3229-1.9258-25.1744
88.8149-0.83252.10429.29280.74775.1343-0.1321-0.3104-0.74050.32970.02320.48710.9416-0.87310.10370.4754-0.17610.0920.4096-0.02770.330129.9197-16.4179-17.895
92.0498-2.8158-0.92215.72710.08052.41050.0168-0.08680.3529-0.2175-0.19330.0852-0.252-0.61960.11070.42340.167-0.03210.2944-0.07810.452729.099517.3866-43.0119
103.4011-0.817-0.1020.2925-0.66374.32790.2139-0.00540.24260.13130.2714-0.2765-0.390.1532-0.50610.31540.0548-0.01830.1877-0.10640.47842.377410.5858-46.6538
115.1569-1.15050.14125.42980.50276.7360.06590.372-0.2713-0.25310.1227-0.09510.0603-0.3806-0.20530.20790.025-0.06170.1944-0.04210.303335.08682.0108-51.1081
127.612-2.7203-1.33824.53162.8045.7462-0.1163-0.5801-0.0281-0.2582-0.06580.02450.0008-0.54960.08980.20220.0028-0.07980.2601-0.03640.355730.2850.9605-40.9634
135.6281-0.0032-1.61429.0634-0.17016.99030.24660.21730.6156-0.4984-0.0808-0.1271-0.3071-0.5787-0.22870.27810.1418-0.04510.328-0.0430.3529.924116.4194-47.0747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 13 )
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 23 )
4X-RAY DIFFRACTION4chain 'A' and (resid 24 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 49 )
6X-RAY DIFFRACTION6chain 'A' and (resid 50 through 74 )
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 87 )
8X-RAY DIFFRACTION8chain 'A' and (resid 88 through 103 )
9X-RAY DIFFRACTION9chain 'B' and (resid -5 through 13 )
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 38 )
11X-RAY DIFFRACTION11chain 'B' and (resid 39 through 69 )
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 103 )

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