[English] 日本語
Yorodumi
- PDB-7apy: Pseudomonas stutzeri nitrous oxide reductase mutant, D576A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7apy
TitlePseudomonas stutzeri nitrous oxide reductase mutant, D576A
ComponentsNitrous-oxide reductase
KeywordsOXIDOREDUCTASE / periplasmic copper-binding protein
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane
Similarity search - Function
Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) ...Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DINUCLEAR COPPER ION / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION / FORMIC ACID / : / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.778 Å
AuthorsZhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)310656 Germany
German Research Foundation (DFG)192904750 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Histidine-Gated Proton-Coupled Electron Transfer to the Cu A Site of Nitrous Oxide Reductase.
Authors: Zhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O.
History
DepositionOct 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrous-oxide reductase
B: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,94526
Polymers143,8292
Non-polymers2,11624
Water16,772931
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15720 Å2
ΔGint-173 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.964, 76.627, 108.563
Angle α, β, γ (deg.)90.000, 93.410, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nitrous-oxide reductase / N(2)OR / N2O reductase


Mass: 71914.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19573, nitrous-oxide reductase

-
Non-polymers , 9 types, 955 molecules

#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CUZ / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION


Mass: 286.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu4S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.36999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36999 Å / Relative weight: 1
ReflectionResolution: 1.778→68.842 Å / Num. obs: 76965 / % possible obs: 90.3 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.181 / Net I/σ(I): 7.6
Reflection shellResolution: 1.783→1.947 Å / Num. unique obs: 3849 / CC1/2: 0.433

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RKZ

6rkz


Resolution: 1.778→68.842 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 7557 5 %
Rwork0.1657 143476 -
obs0.1687 76964 70.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.95 Å2 / Biso mean: 29.7254 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.778→68.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9214 0 88 931 10233
Biso mean--42.75 38.44 -
Num. residues----1172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.889-1.91490.3406970.3011168325
1.9149-1.94230.3476930.3115208131
1.9423-1.97120.32251360.2938243836
1.9712-2.0020.29441670.2835315247
2.002-2.03490.28682000.2711416461
2.0349-2.070.35792970.273505875
2.07-2.10760.29492810.262583786
2.1076-2.14810.32562720.2552613390
2.1481-2.1920.32043800.2496630394
2.192-2.23970.28683510.2367640695
2.2397-2.29180.28273790.2231647796
2.2918-2.34910.26843310.2052639395
2.3491-2.41260.26692900.1969645295
2.4126-2.48360.2862830.1874576985
2.4836-2.56380.24013500.1743649996
2.5638-2.65540.22113220.1787662897
2.6554-2.76170.2343420.1802660397
2.7617-2.88740.22463630.1727658898
2.8874-3.03960.23363310.1644657798
3.0396-3.23010.2293400.1502665798
3.2301-3.47950.20373730.1419664398
3.4795-3.82960.20653860.1202654398
3.8296-4.38370.15793280.1045635194
4.3837-5.52260.16313300.096632893
Refinement TLS params.Method: refined / Origin x: 14.1098 Å / Origin y: 9.907 Å / Origin z: 26.6627 Å
111213212223313233
T-0.0276 Å2-0.0821 Å2-0.0308 Å2-0.0374 Å20.013 Å2--0.0327 Å2
L0.2997 °2-0.0921 °2-0.1793 °2-0.3524 °20.1244 °2--0.4095 °2
S-0.0354 Å °0.0195 Å °-0.0386 Å °-0.1079 Å °0.1214 Å °-0.0299 Å °-0.2324 Å °-0.1442 Å °0.1505 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 638
2X-RAY DIFFRACTION1allA701 - 1315
3X-RAY DIFFRACTION1allB58 - 643
4X-RAY DIFFRACTION1allB701 - 1206
5X-RAY DIFFRACTION1allC1 - 18

+
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