[English] 日本語
Yorodumi
- PDB-1m1p: P21 crystal structure of the tetraheme cytochrome c3 from Shewane... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m1p
TitleP21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1
ComponentsSmall tetraheme cytochrome c
KeywordsELECTRON TRANSPORT / tetraheme cytochrome c
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Tetrahaem cytochrome domain / Cytochrome c3 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Periplasmic tetraheme cytochrome c CctA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLeys, D. / Meyer, T.E. / Tsapin, A.I. / Nealson, K.H. / Cusanovich, M.A. / Van Beeumen, J.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures at atomic resolution reveal the novel concept of 'electron-harvesting' as a role for the small tetraheme cytochrome c
Authors: Leys, D. / Meyer, T.E. / Tsapin, A.I. / Nealson, K.H. / Cusanovich, M.A. / Van Beeumen, J.J.
History
DepositionJun 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
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_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _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 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Apr 3, 2024Group: 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
Remark 999SEQUENCE the sequence of this protein is derived from both N-terminal sequencing and from the ...SEQUENCE the sequence of this protein is derived from both N-terminal sequencing and from the sequenced genome of Shewanella oneidensis strain MR1. The protein sequence is, at present, not available in any protein sequence database.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small tetraheme cytochrome c
B: Small tetraheme cytochrome c
C: Small tetraheme cytochrome c
D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,27034
Polymers58,0426
Non-polymers15,22828
Water20,9151161
1
A: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2446
Polymers9,6741
Non-polymers2,5705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2446
Polymers9,6741
Non-polymers2,5705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2446
Polymers9,6741
Non-polymers2,5705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1485
Polymers9,6741
Non-polymers2,4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1485
Polymers9,6741
Non-polymers2,4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2446
Polymers9,6741
Non-polymers2,5705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
A: Small tetraheme cytochrome c
hetero molecules

C: Small tetraheme cytochrome c
hetero molecules

D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,02628
Polymers48,3685
Non-polymers12,65823
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_566x,y+1,z+11
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area24920 Å2
ΔGint-479 kcal/mol
Surface area23380 Å2
MethodPISA
8
A: Small tetraheme cytochrome c
hetero molecules

C: Small tetraheme cytochrome c
hetero molecules

D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,02628
Polymers48,3685
Non-polymers12,65823
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area24680 Å2
ΔGint-477 kcal/mol
Surface area23630 Å2
MethodPISA
9
A: Small tetraheme cytochrome c
hetero molecules

D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,78322
Polymers38,6944
Non-polymers10,08818
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_566x,y+1,z+11
identity operation1_555x,y,z1
Buried area19640 Å2
ΔGint-374 kcal/mol
Surface area18950 Å2
MethodPISA
10
D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,53916
Polymers29,0213
Non-polymers7,51813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-271 kcal/mol
Surface area14430 Å2
MethodPISA
11
E: Small tetraheme cytochrome c
F: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,39111
Polymers19,3472
Non-polymers5,0449
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-184 kcal/mol
Surface area9980 Å2
MethodPISA
12
D: Small tetraheme cytochrome c
E: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,29510
Polymers19,3472
Non-polymers4,9488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-165 kcal/mol
Surface area9990 Å2
MethodPISA
13
C: Small tetraheme cytochrome c
hetero molecules

D: Small tetraheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,39111
Polymers19,3472
Non-polymers5,0449
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area9420 Å2
ΔGint-183 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.690, 34.005, 108.313
Angle α, β, γ (deg.)90.00, 110.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Small tetraheme cytochrome c


Mass: 9673.621 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Shewanella oneidensis (bacteria) / Strain: Strain MR1 / References: UniProt: Q8EDL6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1161 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulphate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / PH range low: 9.2 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5-3.8 Mammonium sulfate1reservoir
20.1 MBicine1reservoirpH8.5-9.2
330 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→15 Å / Num. all: 91758 / Num. obs: 84418 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.55→1.59 Å / % possible all: 90
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 83876 / Num. measured all: 197538 / Rmerge(I) obs: 0.064

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Identical protein in P212121 spacegroup

Resolution: 1.55→14.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.456 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21148 4456 5 %RANDOM
Rwork0.17265 ---
all0.17458 91750 --
obs0.1745 84418 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.44 Å2
2---0.12 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 1052 1161 5963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215042
X-RAY DIFFRACTIONr_angle_refined_deg1.5732.5427146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39815567
X-RAY DIFFRACTIONr_chiral_restr0.1080.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024040
X-RAY DIFFRACTIONr_nbd_refined0.3570.22674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2747
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.283
X-RAY DIFFRACTIONr_mcbond_it0.8891.52581
X-RAY DIFFRACTIONr_mcangle_it1.56724053
X-RAY DIFFRACTIONr_scbond_it2.23932461
X-RAY DIFFRACTIONr_scangle_it3.2974.53093
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 273
Rwork0.232 4640
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.7
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.59 Å

+
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