[English] 日本語
Yorodumi
- PDB-3fo3: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fo3
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / alpha protein / eight hemes c
Function / homology
Function and homology information


ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / nitrate assimilation / periplasmic space / heme binding / calcium ion binding
Similarity search - Function
Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins ...Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / HEME C / Chem-PG6 / SULFITE ION / THIOSULFATE / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Slutsky, A. / Tikhonova, T.V. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide
Authors: Trofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Safonova, T.N. / Tikhonov, A.V. / Popov, A.N. / Popov, V.O.
History
DepositionDec 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_alt_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_alt_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,35261
Polymers118,9832
Non-polymers16,36959
Water24,9511385
1
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,056183
Polymers356,9486
Non-polymers49,108177
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area115360 Å2
ΔGint-1236 kcal/mol
Surface area92710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.790, 193.790, 193.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-530-

THJ

21A-530-

THJ

31A-531-

NA

41A-533-

TRS

51B-530-

THJ

61B-530-

THJ

71B-531-

NA

81B-533-

TRS

91B-533-

TRS

101A-590-

HOH

111B-590-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59491.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS

-
Non-polymers , 11 types, 1444 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O3S2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26O6
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG400, VAPOR ...Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2004
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.4→12 Å / Num. all: 469642 / Num. obs: 468027 / % possible obs: 99.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OT4

2ot4


Resolution: 1.4→12 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.988 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13946 23479 5 %RANDOM
Rwork0.12595 ---
obs0.12663 443992 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.514 Å2
Refine analyzeLuzzati coordinate error obs: 0.141 Å
Refinement stepCycle: LAST / Resolution: 1.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8217 0 922 1385 10524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0219651
X-RAY DIFFRACTIONr_bond_other_d0.0020.025641
X-RAY DIFFRACTIONr_angle_refined_deg1.5582.15513132
X-RAY DIFFRACTIONr_angle_other_deg0.973313610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95451041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2723.823463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.076151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2131564
X-RAY DIFFRACTIONr_chiral_restr0.0950.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0210624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021864
X-RAY DIFFRACTIONr_nbd_refined0.220.22899
X-RAY DIFFRACTIONr_nbd_other0.2140.27200
X-RAY DIFFRACTIONr_nbtor_refined0.2070.24994
X-RAY DIFFRACTIONr_nbtor_other0.1120.24719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2951
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.259
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.2153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.288
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.150.21
X-RAY DIFFRACTIONr_mcbond_it1.2321.55211
X-RAY DIFFRACTIONr_mcbond_other0.7081.52067
X-RAY DIFFRACTIONr_mcangle_it1.82128380
X-RAY DIFFRACTIONr_scbond_it2.44534866
X-RAY DIFFRACTIONr_scangle_it3.3584.54750
X-RAY DIFFRACTIONr_rigid_bond_restr1.385316296
X-RAY DIFFRACTIONr_sphericity_free7.64131392
X-RAY DIFFRACTIONr_sphericity_bonded3.834314920
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 1754 -
Rwork0.16 32925 -
obs--99.99 %

+
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