[English] 日本語
Yorodumi
- PDB-7usz: Human DDAH-1, holo (Zn-bound) form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7usz
TitleHuman DDAH-1, holo (Zn-bound) form
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE / Cardiovascular enzyme / Proton pump inhibitors / Esomeprazole
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / nitric oxide mediated signal transduction ...dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / nitric oxide mediated signal transduction / catalytic activity / eNOS activation / arginine catabolic process / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / negative regulation of cell population proliferation / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Dimethylarginine dimethylaminohydrolase / N,N dimethylarginine dimethylhydrolase, eukaryotic
Similarity search - Domain/homology
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSmith, C.A. / Ghebre, Y.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R56AR077445 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K01HL118683 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL137703 United States
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2022
Title: Esomeprazole covalently interacts with the cardiovascular enzyme dimethylarginine dimethylaminohydrolase: Insights into the cardiovascular risk of proton pump inhibitors.
Authors: Smith, C.A. / Ebrahimpour, A. / Novikova, L. / Farina, D. / Bailey, A.O. / Russell, W.K. / Jain, A. / Saltzman, A.B. / Malovannaya, A. / Prasad, B.V.V. / Hu, L. / Ghebre, Y.T.
History
DepositionApr 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0566
Polymers62,8542
Non-polymers2024
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.968, 47.634, 146.965
Angle α, β, γ (deg.)90.000, 94.610, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 / DDAH-1 / Dimethylarginine dimethylaminohydrolase 1 / DDAHI / Dimethylargininase-1


Mass: 31427.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH1, DDAH / Production host: Escherichia coli (E. coli) / References: UniProt: O94760, dimethylargininase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl (pH 8.05), 21% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→39.9 Å / Num. obs: 73638 / % possible obs: 98.3 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 11.2
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2000 / CC1/2: 0.704 / Rpim(I) all: 0.531

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JAJ

2jaj


Resolution: 1.65→29.55 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 3696 5.02 %
Rwork0.1508 69873 -
obs0.1532 73569 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.65 Å2 / Biso mean: 25.4029 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.65→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 4 493 4770
Biso mean--58.31 36.78 -
Num. residues----560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.32471510.24672545269694
1.67-1.690.2911650.21642610277598
1.69-1.720.25821500.19682704285499
1.72-1.740.28241340.18372681281599
1.74-1.770.24881260.16532724285099
1.77-1.80.24641580.15652633279198
1.8-1.830.18951340.14322668280298
1.83-1.870.21061450.14762702284798
1.87-1.90.20131560.14012625278198
1.9-1.940.20081430.14582629277297
1.94-1.980.18981330.13042732286599
1.98-2.030.19541240.12932688281299
2.03-2.080.19931340.13212715284999
2.08-2.130.20471400.1312713285399
2.13-2.20.23781280.14122656278498
2.2-2.270.19631470.13462710285798
2.27-2.350.20011340.13472634276897
2.35-2.440.20391400.13472684282499
2.44-2.550.221430.14742721286499
2.55-2.690.20251460.1512720286699
2.69-2.860.21241480.16122691283998
2.86-3.080.23891430.16932648279197
3.08-3.390.19881500.16722748289899
3.39-3.880.16971390.15352753289299
3.88-4.880.16951270.1352732285997
4.88-29.550.16141580.15742807296598

+
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://pdbjlvh1.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