[English] 日本語
Yorodumi
- PDB-9kwu: D98N/C135A mutant of a copper-containing nitrite reductase in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kwu
TitleD98N/C135A mutant of a copper-containing nitrite reductase in complex with nitrite
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper / denitrification
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsFukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom.
Authors: Fukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
History
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 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)36,0189
Polymers35,4901
Non-polymers5288
Water7,116395
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)108,05427
Polymers106,4703
Non-polymers1,58424
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 area11710 Å2
ΔGint-142 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.334, 115.334, 84.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-837-

HOH

21A-855-

HOH

31A-879-

HOH

41A-881-

HOH

-
Components

#1: Protein Copper-containing nitrite reductase


Mass: 35490.012 Da / Num. of mol.: 1 / Mutation: D98N/C135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Gene: nirK, GTNG_0650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4IL26, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M acetate buffer pH 4.5, 5.0% (w/v) PEG 4000, and 75 mM CuSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.12→43 Å / Num. obs: 155451 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 9.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Net I/σ(I): 9.4
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2 / Num. unique obs: 7879 / CC1/2: 0.617 / Rpim(I) all: 0.39 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YSO

4yso


Resolution: 1.12→32.22 Å / SU ML: 0.1149 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 10.5571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1169 7719 4.97 %
Rwork0.1026 147694 -
obs0.1033 155413 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 1.12→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 19 395 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682731
X-RAY DIFFRACTIONf_angle_d1.08313758
X-RAY DIFFRACTIONf_chiral_restr0.0902398
X-RAY DIFFRACTIONf_plane_restr0.0075510
X-RAY DIFFRACTIONf_dihedral_angle_d9.4801385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.3112660.29645084X-RAY DIFFRACTION98.93
1.13-1.150.28353010.26314992X-RAY DIFFRACTION98.79
1.15-1.160.23532340.21985059X-RAY DIFFRACTION98.95
1.16-1.170.20432930.18974999X-RAY DIFFRACTION99.01
1.17-1.190.18312710.16665082X-RAY DIFFRACTION98.95
1.19-1.210.16672570.14855004X-RAY DIFFRACTION98.8
1.21-1.220.14212970.13215012X-RAY DIFFRACTION98.55
1.22-1.240.16382390.12625064X-RAY DIFFRACTION98.51
1.24-1.260.14762700.12224961X-RAY DIFFRACTION98.68
1.26-1.280.12822930.12515067X-RAY DIFFRACTION98.8
1.28-1.30.13632040.13115031X-RAY DIFFRACTION98.59
1.3-1.330.15692420.13625040X-RAY DIFFRACTION98.64
1.33-1.350.14772650.12254980X-RAY DIFFRACTION98.07
1.35-1.380.12392410.09865074X-RAY DIFFRACTION97.95
1.38-1.410.11122220.09424984X-RAY DIFFRACTION97.53
1.41-1.440.10972180.08625004X-RAY DIFFRACTION96.99
1.44-1.480.10612740.08264907X-RAY DIFFRACTION96.28
1.48-1.520.10392180.08044878X-RAY DIFFRACTION95.7
1.52-1.560.0953020.084786X-RAY DIFFRACTION94.85
1.56-1.620.09753070.07974776X-RAY DIFFRACTION94.83
1.62-1.670.09592420.08174828X-RAY DIFFRACTION94.4
1.67-1.740.08022480.07574778X-RAY DIFFRACTION94.16
1.74-1.820.08112010.07694925X-RAY DIFFRACTION94.82
1.82-1.920.09292850.08014737X-RAY DIFFRACTION93.97
1.92-2.030.1022830.08714736X-RAY DIFFRACTION94.11
2.04-2.190.09612750.08934815X-RAY DIFFRACTION94.07
2.19-2.410.10262470.08974796X-RAY DIFFRACTION94.28
2.41-2.760.10912180.09764862X-RAY DIFFRACTION94.6
2.76-3.480.11662630.10174778X-RAY DIFFRACTION93.8
3.48-32.220.12092430.10554655X-RAY DIFFRACTION91.5

+
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