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- PDB-6suv: Horse cytochrome c complexed by octa-anionic calixarene -

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Basic information

Entry
Database: PDB / ID: 6suv
TitleHorse cytochrome c complexed by octa-anionic calixarene
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Complex / host-guest / calixarene
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / lipid binding / apoptotic process / heme binding / identical protein binding / metal ion binding / cytosol
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
ACETYL GROUP / HEME C / octa-anionic calixarene / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsGeremia, S. / Brancatelli, G.
CitationJournal: Org.Biomol.Chem. / Year: 2020
Title: Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene
Authors: Alex, J.M. / Brancatelli, G. / Volpi, S. / Bonaccorso, C. / Casnati, A. / Geremia, S. / Crowley, P.B.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AaA: Cytochrome c
BaB: Cytochrome c
CaC: Cytochrome c
DaD: Cytochrome c
EaE: Cytochrome c
FaF: Cytochrome c
GaG: Cytochrome c
HaH: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,06432
Polymers93,8058
Non-polymers14,25924
Water8,503472
1
AaA: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BaB: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CaC: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DaD: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EaE: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
FaF: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
GaG: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
HaH: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5084
Polymers11,7261
Non-polymers1,7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.591, 65.591, 250.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains A D
44Chains A E
55Chains A F
66Chains A G
77Chains A H
88Chains B C
99Chains B D
1010Chains B E
1111Chains B F
1212Chains B G
1313Chains B H
1414Chains C D
1515Chains C E
1616Chains C F
1717Chains C G
1818Chains C H
1919Chains D E
2020Chains D F
2121Chains D G
2222Chains D H
2323Chains E F
2424Chains E G
2525Chains E H
2626Chains F G
2727Chains F H
2828Chains G H

NCS ensembles :
IDDetails
25EH
1AB
2AC
3AD
4AE
5AF
6AG
7AH
8BC
9BD
10BE
11BF
12BG
13BH
14CD
15CE
16CF
17CG
18CH
19DE
20DF
21DG
22DH
23EF
24EG
26FG
27FH
28GH

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Components

#1: Protein
Cytochrome c


Mass: 11725.598 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Equus caballus (horse) / References: UniProt: P00004
#2: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical
ChemComp-LVQ / octa-anionic calixarene


Mass: 1119.857 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H37AsNaO25S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4988
pseudo-merohedral22-K, -H, -L20.5012
ReflectionResolution: 2.5→46.38 Å / Num. obs: 34903 / % possible obs: 96.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.101 / Rrim(I) all: 0.178 / Χ2: 0.83 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3775 / CC1/2: 0.739 / Rpim(I) all: 0.243 / Rrim(I) all: 0.4 / Χ2: 0.58 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DENZOdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→46.38 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.845 / SU B: 6.473 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / ESU R: 0.238 / ESU R Free: 0.063
RfactorNum. reflection% reflection
Rfree0.2366 1791 5.132 %
Rwork0.1695 --
all0.173 --
obs-34902 96.096 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.085 Å2-0 Å2-0 Å2
2---14.085 Å2-0 Å2
3---28.171 Å2
Refinement stepCycle: LAST / Resolution: 2.502→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 920 472 7976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137792
X-RAY DIFFRACTIONr_angle_refined_deg3.3461.9610784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98323.919296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.676151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.2211516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025792
X-RAY DIFFRACTIONr_nbd_refined0.2230.23732
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2430
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2920.214
X-RAY DIFFRACTIONr_mcbond_it1.9932.5613336
X-RAY DIFFRACTIONr_mcangle_it3.1553.8254152
X-RAY DIFFRACTIONr_scbond_it2.2172.5534456
X-RAY DIFFRACTIONr_scangle_it3.283.7646632
X-RAY DIFFRACTIONr_lrange_it6.37832.4412626
X-RAY DIFFRACTIONr_ncsr_local_group_10.0120.053329
X-RAY DIFFRACTIONr_ncsr_local_group_20.0310.053330
X-RAY DIFFRACTIONr_ncsr_local_group_30.0150.053333
X-RAY DIFFRACTIONr_ncsr_local_group_40.0190.053328
X-RAY DIFFRACTIONr_ncsr_local_group_50.0260.053324
X-RAY DIFFRACTIONr_ncsr_local_group_60.0140.053334
X-RAY DIFFRACTIONr_ncsr_local_group_70.0170.053337
X-RAY DIFFRACTIONr_ncsr_local_group_80.030.053318
X-RAY DIFFRACTIONr_ncsr_local_group_90.0140.053325
X-RAY DIFFRACTIONr_ncsr_local_group_100.0170.053328
X-RAY DIFFRACTIONr_ncsr_local_group_110.0260.053317
X-RAY DIFFRACTIONr_ncsr_local_group_120.010.053330
X-RAY DIFFRACTIONr_ncsr_local_group_130.0180.053327
X-RAY DIFFRACTIONr_ncsr_local_group_140.0250.053319
X-RAY DIFFRACTIONr_ncsr_local_group_150.0290.053316
X-RAY DIFFRACTIONr_ncsr_local_group_160.0390.053314
X-RAY DIFFRACTIONr_ncsr_local_group_170.0260.053322
X-RAY DIFFRACTIONr_ncsr_local_group_180.0280.053327
X-RAY DIFFRACTIONr_ncsr_local_group_190.020.053325
X-RAY DIFFRACTIONr_ncsr_local_group_200.0250.053310
X-RAY DIFFRACTIONr_ncsr_local_group_210.0140.053333
X-RAY DIFFRACTIONr_ncsr_local_group_220.020.053333
X-RAY DIFFRACTIONr_ncsr_local_group_230.0310.053310
X-RAY DIFFRACTIONr_ncsr_local_group_240.0190.053327
X-RAY DIFFRACTIONr_ncsr_local_group_250.0230.053322
X-RAY DIFFRACTIONr_ncsr_local_group_260.0270.053321
X-RAY DIFFRACTIONr_ncsr_local_group_270.0290.053322
X-RAY DIFFRACTIONr_ncsr_local_group_280.0180.053329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-2.5670.4171230.2472286X-RAY DIFFRACTION90.2924
2.567-2.6370.2941080.2012391X-RAY DIFFRACTION95.2363
2.637-2.7130.2861380.1922284X-RAY DIFFRACTION95.4671
2.713-2.7970.2881020.1962248X-RAY DIFFRACTION95.9967
2.797-2.8880.311150.192157X-RAY DIFFRACTION95.4622
2.888-2.9890.2521060.1742168X-RAY DIFFRACTION96.4377
2.989-3.1020.2891160.1742045X-RAY DIFFRACTION97.3423
3.102-3.2280.308950.2011972X-RAY DIFFRACTION97.5
3.228-3.3710.2481010.1971858X-RAY DIFFRACTION94.9588
3.371-3.5360.1931040.1661813X-RAY DIFFRACTION96.8182
3.536-3.7260.183940.1591718X-RAY DIFFRACTION96.6916
3.726-3.9510.2790.151644X-RAY DIFFRACTION97.8421
3.951-4.2230.1951000.1451555X-RAY DIFFRACTION97.8132
4.223-4.560.197670.1251444X-RAY DIFFRACTION98.2445
4.56-4.9930.169850.1241331X-RAY DIFFRACTION97.5207
4.993-5.5780.209700.1451189X-RAY DIFFRACTION96.9207
5.578-6.4330.192590.161040X-RAY DIFFRACTION95.8152
6.433-7.860.289670.169870X-RAY DIFFRACTION96.7975
7.86-11.0370.188500.182691X-RAY DIFFRACTION97.6285
11.037-46.380.313120.193407X-RAY DIFFRACTION96.9907

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