[English] 日本語
Yorodumi
- PDB-9fui: CRYSTAL STRUCTURE OF NITRIC OXIDE TREATED F295L MUTANT OF THREE-D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fui
TitleCRYSTAL STRUCTURE OF NITRIC OXIDE TREATED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Nitrite reductase, copper-type / Cytochrome c / Multicopper oxidase, N-terminal / Multicopper oxidase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / HEME C / NITRIC OXIDE / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.17 Å
AuthorsPetchyam, N. / Antonyuk, S. / Hasnain, S.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/N013972/1 United Kingdom
UK Research and Innovation (UKRI)BB/L006960/1 United Kingdom
CitationJournal: To Be Published
Title: Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7458
Polymers48,8791
Non-polymers8667
Water13,962775
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,23524
Polymers146,6383
Non-polymers2,59721
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19980 Å2
ΔGint-247 kcal/mol
Surface area44040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.275, 128.275, 86.348
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-197-

ARG

21A-1254-

HOH

31A-1261-

HOH

41A-1330-

HOH

51A-1331-

HOH

61A-1344-

HOH

71A-1366-

HOH

-
Components

#1: Protein Copper-containing nitrite reductase


Mass: 48879.348 Da / Num. of mol.: 1 / Mutation: F295L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: nirK, D7S62_04310 / Details (production host): pET26b-F295L_RpNiR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NAW4, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.86999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86999 Å / Relative weight: 1
ReflectionResolution: 1.17→37.057 Å / Num. obs: 173732 / % possible obs: 97.2 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Χ2: 0.77 / Net I/σ(I): 10.3
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1 / Num. unique obs: 6454 / CC1/2: 0.504 / Rpim(I) all: 0.588 / Rrim(I) all: 1.043 / Χ2: 0.58 / % possible all: 73.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.17→37.057 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / WRfactor Rfree: 0.12 / WRfactor Rwork: 0.097 / SU B: 1.052 / SU ML: 0.02 / Average fsc free: 0.9837 / Average fsc work: 0.9874 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.1274 8589 4.945 %RANDOM
Rwork0.1052 165115 --
all0.106 ---
obs-173704 97.174 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.111 Å20.056 Å2-0 Å2
2--0.111 Å2-0 Å2
3----0.362 Å2
Refinement stepCycle: LAST / Resolution: 1.17→37.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 53 775 4265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124054
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163860
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.855601
X-RAY DIFFRACTIONr_angle_other_deg0.681.7628993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.199520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14210685
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.12510180
X-RAY DIFFRACTIONr_chiral_restr0.0980.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024952
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02932
X-RAY DIFFRACTIONr_nbd_refined0.2590.2757
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23390
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21856
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2595
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.240
X-RAY DIFFRACTIONr_nbd_other0.2160.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2710.287
X-RAY DIFFRACTIONr_mcbond_it3.3941.281992
X-RAY DIFFRACTIONr_mcbond_other3.3641.2771987
X-RAY DIFFRACTIONr_mcangle_it4.7712.3122521
X-RAY DIFFRACTIONr_mcangle_other4.7722.3142522
X-RAY DIFFRACTIONr_scbond_it4.7341.4452062
X-RAY DIFFRACTIONr_scbond_other4.7351.4452060
X-RAY DIFFRACTIONr_scangle_it6.6842.5833019
X-RAY DIFFRACTIONr_scangle_other6.6842.5833019
X-RAY DIFFRACTIONr_lrange_it19.22622.7224918
X-RAY DIFFRACTIONr_lrange_other13.62216.4094549
X-RAY DIFFRACTIONr_rigid_bond_restr3.36937914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.17-1.20.2545300.24493930.244132050.9540.95875.14580.239
1.2-1.2330.2315500.228107350.228128890.9640.96487.55530.219
1.233-1.2690.2025610.197118380.197125180.9730.97599.04940.184
1.269-1.3080.1996620.175115080.176121740.9760.98199.96710.157
1.308-1.3510.1745540.155112010.156117600.9810.98699.95750.136
1.351-1.3980.1585980.135108510.136114530.9850.98999.96510.116
1.398-1.4510.1495810.12103610.121109500.9870.99199.92690.101
1.451-1.510.1484950.106101400.108106410.9870.99399.94360.089
1.51-1.5770.1214600.08596560.087101200.9910.99599.96050.073
1.577-1.6540.1064810.07392390.07497230.9930.99799.96910.062
1.654-1.7430.114130.07787880.07992040.9870.99699.96740.068
1.743-1.8490.0954290.0783470.07187770.9940.99799.98860.063
1.849-1.9760.1083910.08178130.08282040.9930.9961000.076
1.976-2.1340.1073640.08372860.08576500.9930.9961000.081
2.134-2.3370.1113540.07967060.08170610.9930.99699.98580.079
2.337-2.6110.0933300.07660100.07763400.9950.9961000.078
2.611-3.0120.1043050.08652840.08755900.9930.99599.98210.093
3.012-3.6830.1142460.09545130.09647590.9930.9951000.108
3.683-5.1840.1171680.10835000.10936680.9930.9941000.128
5.184-37.0570.1871170.18319460.18320630.9850.9861000.206

+
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