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- PDB-1m1p: P21 crystal structure of the tetraheme cytochrome c3 from Shewane... -

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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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 1161 / Source method: isolated from a natural source / Formula: H2O
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: 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

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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

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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

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