[English] 日本語
Yorodumi
- PDB-9ixe: Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ixe
TitleCrystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase without oxidized Cys86
ComponentsN(omega)-hydroxy-L-arginine amidinohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


Nomega-hydroxy-L-arginine amidinohydrolase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / arginase activity / : / antibiotic biosynthetic process / manganese ion binding / cytosol
Similarity search - Function
Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
COPPER (I) ION / : / N(omega)-hydroxy-L-arginine amidinohydrolase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Copper inactivates DcsB by oxidizing the metal ligand Cys86 to sulfinic acid.
Authors: Oda, K. / Komaguchi, K. / Matoba, Y.
History
DepositionJul 27, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 20, 2024ID: 9IQ9
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jan 1, 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: N(omega)-hydroxy-L-arginine amidinohydrolase
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3588
Polymers60,0332
Non-polymers3256
Water9,836546
1
A: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1514
Polymers30,0171
Non-polymers1343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11550 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2074
Polymers30,0171
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-23 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.502, 46.981, 59.559
Angle α, β, γ (deg.)83.57, 84.69, 70.09
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein N(omega)-hydroxy-L-arginine amidinohydrolase / hydroxyarginase


Mass: 30016.701 Da / Num. of mol.: 2 / Fragment: N(omega)-hydroxy-L-arginine amidinohydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: dcsB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: PEG 4000, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.35 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35 Å / Relative weight: 1
ReflectionResolution: 1.58→43.65 Å / Num. obs: 59923 / % possible obs: 93 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.061 / Rrim(I) all: 0.09 / Χ2: 0.73 / Net I/σ(I): 6.2 / Num. measured all: 122601
Reflection shellResolution: 1.58→1.61 Å / % possible obs: 86.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.475 / Num. measured all: 5828 / Num. unique obs: 2774 / CC1/2: 0.648 / Rpim(I) all: 0.439 / Rrim(I) all: 0.648 / Χ2: 0.85 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→43.65 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 3085 5.15 %
Rwork0.179 --
obs0.181 59912 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 6 546 4619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064250
X-RAY DIFFRACTIONf_angle_d0.8075820
X-RAY DIFFRACTIONf_dihedral_angle_d18.689611
X-RAY DIFFRACTIONf_chiral_restr0.055669
X-RAY DIFFRACTIONf_plane_restr0.006782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.29331310.26532404X-RAY DIFFRACTION86
1.6-1.630.25871350.24082490X-RAY DIFFRACTION90
1.63-1.660.23681330.21442449X-RAY DIFFRACTION89
1.66-1.690.26931270.20962535X-RAY DIFFRACTION91
1.69-1.720.27011040.19462564X-RAY DIFFRACTION90
1.72-1.760.21291600.19892500X-RAY DIFFRACTION92
1.76-1.80.22811350.18872572X-RAY DIFFRACTION91
1.8-1.840.24051600.18732503X-RAY DIFFRACTION92
1.84-1.880.241300.18922568X-RAY DIFFRACTION92
1.88-1.930.22391120.18122618X-RAY DIFFRACTION92
1.93-1.990.21761430.18692580X-RAY DIFFRACTION93
1.99-2.050.26651470.18132579X-RAY DIFFRACTION93
2.05-2.130.19571130.18182623X-RAY DIFFRACTION93
2.13-2.210.21331510.17322565X-RAY DIFFRACTION93
2.21-2.310.19171490.1752585X-RAY DIFFRACTION94
2.31-2.440.22091580.18662597X-RAY DIFFRACTION94
2.44-2.590.23751220.18172654X-RAY DIFFRACTION95
2.59-2.790.22051470.18212672X-RAY DIFFRACTION96
2.79-3.070.23641300.18432704X-RAY DIFFRACTION96
3.07-3.510.22111500.1642680X-RAY DIFFRACTION97
3.51-4.430.1861870.15432684X-RAY DIFFRACTION98
4.43-43.650.19761610.17472701X-RAY DIFFRACTION98

+
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