[English] 日本語
Yorodumi
- PDB-9cuf: Room temperature SSX structure of ccNiR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cuf
TitleRoom temperature SSX structure of ccNiR
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT / cytochrome c nitrite reductase
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 / iron ion binding / heme binding / calcium ion binding
Similarity search - Function
Formate-dependent cytochrome c nitrite reductase, c552 subunit / Cytochrome c552 / Cytochrome c552 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily
Similarity search - Domain/homology
HEME C / Chem-PE3 / Cytochrome c-552
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMalla, T.N. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Iucrj / Year: 2025
Title: Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization.
Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. ...Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. / Orlans, J. / Basu, S. / de Sanctis, D. / Schmidt, M.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,03515
Polymers99,1352
Non-polymers6,90013
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-260 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.840, 95.470, 228.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

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


Mass: 49567.418 Da / Num. of mol.: 2 / Fragment: UNP residues 28-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: nrfA, SO_3980 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8EAC7, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5 / Details: 40% PEG 4K, 200 mM sodium malonate, 100 mM MES

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.12 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Sep 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 3.3→59.49 Å / Num. obs: 17548 / % possible obs: 100 % / Redundancy: 19.37 % / Biso Wilson estimate: 113.46 Å2 / CC1/2: 0.95 / Net I/σ(I): 4.3
Reflection shellResolution: 3.3→3.39 Å / Num. unique obs: 860 / CC1/2: 0.18

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata scaling
PHASERphasing
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→59.49 Å / SU ML: 0.709 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2982 1657 9.92 %
Rwork0.2122 15046 -
obs0.2206 16703 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.63 Å2
Refinement stepCycle: LAST / Resolution: 3.3→59.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6946 0 475 0 7421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01157658
X-RAY DIFFRACTIONf_angle_d1.433610463
X-RAY DIFFRACTIONf_chiral_restr0.051004
X-RAY DIFFRACTIONf_plane_restr0.00861302
X-RAY DIFFRACTIONf_dihedral_angle_d19.62192802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40.39761060.3546964X-RAY DIFFRACTION73.9
3.4-3.510.3623950.3961940X-RAY DIFFRACTION74.41
3.51-3.630.48041710.36021250X-RAY DIFFRACTION97.93
3.63-3.780.40341360.3351257X-RAY DIFFRACTION98.93
3.78-3.950.35981550.29261285X-RAY DIFFRACTION100
3.95-4.160.3521330.25461309X-RAY DIFFRACTION99.93
4.16-4.420.32831400.23711283X-RAY DIFFRACTION99.86
4.42-4.760.32631310.19591334X-RAY DIFFRACTION99.93
4.76-5.240.26731250.1841320X-RAY DIFFRACTION99.93
5.24-5.990.29521390.191340X-RAY DIFFRACTION100
6-7.540.26991530.18631338X-RAY DIFFRACTION100
7.55-59.490.21671730.13761426X-RAY DIFFRACTION99.94

+
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