[English] 日本語
Yorodumi
- PDB-3l1t: E. coli NrfA sulfite ocmplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l1t
TitleE. coli NrfA sulfite ocmplex
ComponentsCytochrome c-552
KeywordsOXIDOREDUCTASE / multiheme / sulfite / nitrite reductase / c-type cytochrome / Electron transport / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


nitric oxide reductase activity / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / iron ion binding / calcium ion binding / heme binding
Similarity search - Function
Formate-dependent cytochrome c nitrite reductase, c552 subunit / 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 / Up-down Bundle ...Formate-dependent cytochrome c nitrite reductase, c552 subunit / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / SULFITE ION / Cytochrome c-552
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsClarke, T.A. / Hemmings, A.M. / Butt, J.N.
CitationJournal: Biochem.J. / Year: 2010
Title: Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli
Authors: Kemp, G.L. / Clarke, T.A. / Marritt, S.J. / Lockwood, C. / Poock, S.R. / Hemmings, A.M. / Richardson, D.J. / Cheesman, M.R. / Butt, J.N.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c-552
B: Cytochrome c-552
C: Cytochrome c-552
D: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,50849
Polymers202,6724
Non-polymers13,83645
Water17,240957
1
A: Cytochrome c-552
B: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,17023
Polymers101,3362
Non-polymers6,83421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-11 kcal/mol
Surface area38130 Å2
MethodPISA
2
C: Cytochrome c-552
D: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33826
Polymers101,3362
Non-polymers7,00224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-13 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.520, 82.234, 142.172
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome c-552 / Ammonia-forming cytochrome c nitrite reductase / Cytochrome c nitrite reductase


Mass: 50668.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12, JCB2048
References: UniProt: P0ABK9, nitrite reductase (cytochrome; ammonia-forming)

-
Non-polymers , 5 types, 1002 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 20% PEG 10K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2005
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→60.9 Å / Num. all: 91009 / Num. obs: 91009 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.086 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 13192 / Rsym value: 0.425 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RDZ

2rdz


Resolution: 2.3→50.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.706 / SU ML: 0.164 / Isotropic thermal model: Individual Atom Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23809 4553 5 %RANDOM
Rwork0.17661 ---
obs0.17971 86417 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.168 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 936 957 15797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215359
X-RAY DIFFRACTIONr_angle_refined_deg1.2332.11621046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4451778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72724.979701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.175152486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9811572
X-RAY DIFFRACTIONr_chiral_restr0.0760.22021
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111948
X-RAY DIFFRACTIONr_mcbond_it0.4981.58840
X-RAY DIFFRACTIONr_mcangle_it0.959214173
X-RAY DIFFRACTIONr_scbond_it1.58936519
X-RAY DIFFRACTIONr_scangle_it2.4844.56867
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 329 -
Rwork0.229 6329 -
obs--99.37 %

+
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