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Basic information

Entry
Database: PDB / ID: 4rsz
TitleThe X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT
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 / respirasome / 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 / respirasome / 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-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
Cisplatin / HEME C / NITRATE ION / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMerlino, A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: The X-ray structure of the primary adducts formed in the reaction between cisplatin and cytochrome c.
Authors: Ferraro, G. / Messori, L. / Merlino, A.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_asym_id / _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_asym_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_asym_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 / _pdbx_validate_close_contact.auth_comp_id_2 / _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 / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
C: Cytochrome c
D: Cytochrome c
E: Cytochrome c
F: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,74935
Polymers70,3546
Non-polymers6,39529
Water2,288127
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7685
Polymers11,7261
Non-polymers1,0434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9267
Polymers11,7261
Non-polymers1,2016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5926
Polymers11,7261
Non-polymers8675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7685
Polymers11,7261
Non-polymers1,0434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8306
Polymers11,7261
Non-polymers1,1055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8646
Polymers11,7261
Non-polymers1,1395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: Cytochrome c
hetero molecules

D: Cytochrome c
F: Cytochrome c
hetero molecules

A: Cytochrome c
B: Cytochrome c
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,74935
Polymers70,3546
Non-polymers6,39529
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_344-x+y-2,-x-1,z-11
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area19760 Å2
ΔGint-232 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.344, 120.344, 36.673
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 1 - 104 / Label seq-ID: 1 - 104

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Cytochrome c /


Mass: 11725.598 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004

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Non-polymers , 5 types, 156 molecules

#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion ...Details: A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 21, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→104.22 Å / Num. all: 30538 / Num. obs: 30538 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.109

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1HRC
Resolution: 2.19→104.22 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.786 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28211 1544 5.1 %RANDOM
Rwork0.23144 ---
all0.23403 28987 --
obs0.23403 28987 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å2-0 Å2
3---2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.19→104.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 347 127 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195450
X-RAY DIFFRACTIONr_bond_other_d0.0080.025241
X-RAY DIFFRACTIONr_angle_refined_deg1.8452.0547317
X-RAY DIFFRACTIONr_angle_other_deg1.4313.00212126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7625.34206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.446151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.9121512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0216050
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021189
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_it1.6291.9472500
X-RAY DIFFRACTIONr_mcbond_other1.6291.9482499
X-RAY DIFFRACTIONr_mcangle_it2.6882.9113118
X-RAY DIFFRACTIONr_mcangle_other2.6872.913119
X-RAY DIFFRACTIONr_scbond_it2.2762.1062950
X-RAY DIFFRACTIONr_scbond_other2.2272.0852903
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1022.9854152
X-RAY DIFFRACTIONr_long_range_B_refined5.88415.5056874
X-RAY DIFFRACTIONr_long_range_B_other5.84815.4486848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62850.11
12B62850.11
21A63250.11
22C63250.11
31A62090.11
32D62090.11
41A62220.1
42E62220.1
51A62940.11
52F62940.11
61B62680.1
62C62680.1
71B62430.09
72D62430.09
81B61670.1
82E61670.1
91B62810.09
92F62810.09
101C62600.1
102D62600.1
111C62340.09
112E62340.09
121C63310.1
122F63310.1
131D62420.1
132E62420.1
141D63430.08
142F63430.08
151E62480.09
152F62480.09
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 114 -
Rwork0.309 2124 -
obs--97.81 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.76880.01590.01911.4210.62970.3832-0.0585-0.0358-0.2311-0.1775-0.09490.1336-0.2033-0.02960.15340.26650.0338-0.05270.1786-0.0470.2037-90.9794-0.311718.3381
23.64540.9321.04141.53310.44250.3965-0.4309-0.22490.2145-0.68020.2465-0.1584-0.2353-0.01140.18440.4296-0.04540.02930.1043-0.02810.2751-73.146118.10420.0515
30.62440.0397-0.48661.77830.20490.4601-0.0345-0.0498-0.2128-0.57470.0442-0.727-0.103-0.0334-0.00970.2787-0.01470.28140.16830.0180.4756-66.0765-6.367115.9623
43.0940.52420.66552.20490.43370.22860.3172-0.42430.39140.1662-0.40330.18070.1383-0.1470.08610.1308-0.12860.05950.3379-0.16350.1908-104.6333-16.312534.8594
56.4221-3.2503-1.26841.68410.63430.2523-0.7533-1.64930.92170.3260.9238-0.48290.16640.3131-0.17050.30340.1639-0.18030.655-0.34360.2698-90.299431.437535.6297
64.02170.7520.32440.7142-0.65461.40490.3096-0.6375-0.8887-0.0021-0.1852-0.3824-0.2096-0.1561-0.12440.29120.01120.07250.21310.28080.5851-84.8421-32.031431.2018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B1 - 201
3X-RAY DIFFRACTION3C1 - 201
4X-RAY DIFFRACTION4D1 - 201
5X-RAY DIFFRACTION5E1 - 201
6X-RAY DIFFRACTION6F1 - 201

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