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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sce
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / eight hemes c / nitrite reductase / Tyr-Gln and Tyr-Cys bonds
Function / homology
Function and homology information


: / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded 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
HEME C / Chem-PG6 / PHOSPHATE ION / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity.
Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Tikhonov, A.V. / Safonova, T.N. / Boyko, K.M. / Dorovatovskii, P.V. / Popov, V.O.
History
DepositionJun 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Sep 13, 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 / 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 / _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 1.5Nov 6, 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)132,59149
Polymers117,6692
Non-polymers14,92147
Water21,3661186
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)397,772147
Polymers353,0086
Non-polymers44,764141
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 area108440 Å2
ΔGint-1189 kcal/mol
Surface area96180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.000, 193.000, 193.000
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-527-

PO4

21A-527-

PO4

31B-527-

PO4

41B-527-

PO4

51A-958-

HOH

61A-993-

HOH

71B-1022-

HOH

81B-1058-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 58834.641 Da / Num. of mol.: 2 / Fragment: UNP residues 33-551 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: ALEN 2
References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS, Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor

-
Non-polymers , 7 types, 1233 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O6
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1186 / 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: 5.09 Å3/Da / Density % sol: 75.84 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Protein solution (2.5 uL): 9.3 mg/mL TvNiRb, 0.1 M potassium phosphate, pH 7.0, Reservoir solution (2.5 uL): 0.2 M tri-sodium citrate dihydrate, 0.1 M Tris hydrochloride, pH8.5, 30% v/v ...Details: Protein solution (2.5 uL): 9.3 mg/mL TvNiRb, 0.1 M potassium phosphate, pH 7.0, Reservoir solution (2.5 uL): 0.2 M tri-sodium citrate dihydrate, 0.1 M Tris hydrochloride, pH8.5, 30% v/v PEG400 , VAPOR DIFFUSION, HANGING DROP, temperature 278.0 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.75
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.45→136.472 Å / Num. obs: 464187 / % possible obs: 99.9 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 1.45→1.6 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OT4

2ot4


Resolution: 1.45→100 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.146 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14041 20931 5 %RANDOM
Rwork0.12385 ---
obs0.12468 397225 99.91 %-
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: 14.342 Å2
Refine analyzeLuzzati coordinate error obs: 0.139 Å
Refinement stepCycle: LAST / Resolution: 1.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8231 0 867 1186 10284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0219648
X-RAY DIFFRACTIONr_bond_other_d0.0010.025894
X-RAY DIFFRACTIONr_angle_refined_deg1.462.1513125
X-RAY DIFFRACTIONr_angle_other_deg1.098314231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12251038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48823.869473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.959151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191565
X-RAY DIFFRACTIONr_chiral_restr0.0890.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0210676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021899
X-RAY DIFFRACTIONr_mcbond_it1.2161.5562
X-RAY DIFFRACTIONr_mcbond_other0.6481.5221
X-RAY DIFFRACTIONr_mcangle_it1.9812919
X-RAY DIFFRACTIONr_scbond_it2.9633370
X-RAY DIFFRACTIONr_scangle_it4.4154.5324
X-RAY DIFFRACTIONr_rigid_bond_restr1.794315542
X-RAY DIFFRACTIONr_sphericity_free7.42931188
X-RAY DIFFRACTIONr_sphericity_bonded4.147315161
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 1543 -
Rwork0.185 29161 -
obs--99.9 %

+
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