[English] 日本語
Yorodumi
- PDB-5gyr: Tetrameric Allochromatium vinosum cytochrome c' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gyr
TitleTetrameric Allochromatium vinosum cytochrome c'
ComponentsCytochrome c'
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYamanaka, M. / Hoshizumi, M. / Nagao, S. / Nakayama, R. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
MEXTJP26288080 Japan
MEXTJP15K13744 Japan
MEXTJP15H00945 Japan
MEXTJP16K17935 Japan
CitationJournal: Protein Sci. / Year: 2017
Title: Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers
Authors: Yamanaka, M. / Hoshizumi, M. / Nagao, S. / Nakayama, R. / Shibata, N. / Higuchi, Y. / Hirota, S.
History
DepositionSep 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / 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 / _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 / _diffrn_source.pdbx_synchrotron_site / _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.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 8, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
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.pdbx_value_order / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c'
B: Cytochrome c'
E: Cytochrome c'
F: Cytochrome c'
I: Cytochrome c'
J: Cytochrome c'
M: Cytochrome c'
N: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,40016
Polymers110,4518
Non-polymers4,9488
Water14,556808
1
A: Cytochrome c'
B: Cytochrome c'
M: Cytochrome c'
N: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7008
Polymers55,2264
Non-polymers2,4744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-154 kcal/mol
Surface area24750 Å2
MethodPISA
2
E: Cytochrome c'
F: Cytochrome c'
I: Cytochrome c'
J: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7008
Polymers55,2264
Non-polymers2,4744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-156 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.949, 48.620, 130.550
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23F
14A
24I
15A
25J
16A
26M
17A
27N
18B
28E
19B
29F
110B
210I
111B
211J
112B
212M
113B
213N
114E
214F
115E
215I
116E
216J
117E
217M
118E
218N
119F
219I
120F
220J
121F
221M
122F
222N
123I
223J
124I
224M
125I
225N
126J
226M
127J
227N
128M
228N

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 131 / Label seq-ID: 1 - 131

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22EC
13AA
23FD
14AA
24IE
15AA
25JF
16AA
26MG
17AA
27NH
18BB
28EC
19BB
29FD
110BB
210IE
111BB
211JF
112BB
212MG
113BB
213NH
114EC
214FD
115EC
215IE
116EC
216JF
117EC
217MG
118EC
218NH
119FD
219IE
120FD
220JF
121FD
221MG
122FD
222NH
123IE
223JF
124IE
224MG
125IE
225NH
126JF
226MG
127JF
227NH
128MG
228NH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

#1: Protein
Cytochrome c'


Mass: 13806.436 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (bacteria)
Strain: ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D
Gene: cycA, Alvin_2765 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P00154
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1mM sodium acetate, 0.2mM ammonium acetate, 30% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→41.4 Å / Num. obs: 135869 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.9 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bbh

1bbh


Resolution: 1.6→41.4 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.976 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23228 6704 4.9 %RANDOM
Rwork0.20406 ---
obs0.20546 129158 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20.18 Å2
2--2.02 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.6→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 344 808 8888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198248
X-RAY DIFFRACTIONr_bond_other_d0.0070.027648
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.00511224
X-RAY DIFFRACTIONr_angle_other_deg1.387317536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.11851040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26325.778360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.277151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7871532
X-RAY DIFFRACTIONr_chiral_restr0.0780.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029824
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021904
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_it3.5542.4944184
X-RAY DIFFRACTIONr_mcbond_other3.5512.4934183
X-RAY DIFFRACTIONr_mcangle_it4.3493.7385216
X-RAY DIFFRACTIONr_mcangle_other4.3493.7385217
X-RAY DIFFRACTIONr_scbond_it3.6732.6914064
X-RAY DIFFRACTIONr_scbond_other3.6732.6914062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4273.8966008
X-RAY DIFFRACTIONr_long_range_B_refined5.15320.41910849
X-RAY DIFFRACTIONr_long_range_B_other4.90119.93910429
X-RAY DIFFRACTIONr_rigid_bond_restr5.015315896
X-RAY DIFFRACTIONr_sphericity_free33.2515250
X-RAY DIFFRACTIONr_sphericity_bonded14.602516286
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62060.13
12B62060.13
21A66110.06
22E66110.06
31A62000.13
32F62000.13
41A61110.14
42I61110.14
51A63390.12
52J63390.12
61A60830.14
62M60830.14
71A63590.11
72N63590.11
81B61800.13
82E61800.13
91B71330.07
92F71330.07
101B66600.13
102I66600.13
111B61740.13
112J61740.13
121B66450.14
122M66450.14
131B62250.13
132N62250.13
141E61800.13
142F61800.13
151E61330.14
152I61330.14
161E63520.12
162J63520.12
171E61360.15
172M61360.15
181E63420.12
182N63420.12
191F66730.13
192I66730.13
201F62000.13
202J62000.13
211F66690.13
212M66690.13
221F62450.13
222N62450.13
231I60970.15
232J60970.15
241I70070.1
242M70070.1
251I60980.14
252N60980.14
261J60770.15
262M60770.15
271J65360.08
272N65360.08
281M60970.14
282N60970.14
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 527 -
Rwork0.27 9261 -
obs--97.24 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more