[English] 日本語
Yorodumi
- PDB-2ci3: Crystal Structure of Dimethylarginine dimethylaminohydrolase crys... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ci3
TitleCrystal Structure of Dimethylarginine dimethylaminohydrolase crystal form I
ComponentsNG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
KeywordsHYDROLASE / NOS REGULATION / S-NITROSYLATION / ZINC / NO / MMA / ADMA
Function / homology
Function and homology information


protein nitrosylation / eNOS activation / dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / nitric oxide biosynthetic process / positive regulation of nitric oxide biosynthetic process / zinc ion binding
Similarity search - Function
Dimethylarginine dimethylaminohydrolase / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFrey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G.
CitationJournal: Structure / Year: 2006
Title: Structure of the Mammalian Nos Regulator Dimethylarginine Dimethylaminohydrolase: A Basis for the Design of Specific Inhibitors.
Authors: Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G.
History
DepositionMar 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1


Theoretical massNumber of molelcules
Total (without water)31,1991
Polymers31,1991
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.461, 79.619, 44.879
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1 / DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I / DIMETHYLARGININASE 1 / DDAHI / DDAH-1


Mass: 31198.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: BRAIN / References: UniProt: P56965, dimethylargininase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42.6 %
Crystal growpH: 5
Details: 100 MM CITRIC ACID/NAOH, 20-40% PEG 8000, 2 MM TCEP, PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 28708 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.8 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H70

1h70


Resolution: 1.7→19.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 931832.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1392 4.9 %RANDOM
Rwork0.188 ---
obs0.188 28617 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0952 Å2 / ksol: 0.34706 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å21.97 Å2
2---0.92 Å20 Å2
3---1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 0 349 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 239 5 %
Rwork0.257 4563 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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