[English] 日本語
Yorodumi
- PDB-6jv0: Crystal Structure of N-terminal domain of ArgZ, bound to Product,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jv0
TitleCrystal Structure of N-terminal domain of ArgZ, bound to Product, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria
ComponentsSll1336 protein
KeywordsHYDROLASE / arginine dihydrolase / amidino-transferase domain / alpha/beta propeller fold
Function / homology
Function and homology information


: / : / Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold / Arginine dihydrolase ArgZ-like, C-terminal, first region / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / LOR/SDH bifunctional enzyme conserved region / N,N dimethylarginine dimethylhydrolase, eukaryotic / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
L-ornithine / Sll1336 protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.14 Å
AuthorsZhuang, N. / Li, L. / Wu, X. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822001 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism.
Authors: Zhuang, N. / Zhang, H. / Li, L. / Wu, X. / Yang, C. / Zhang, Y.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sll1336 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,76419
Polymers34,5761
Non-polymers1,18718
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.468, 87.746, 43.310
Angle α, β, γ (deg.)90.000, 94.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Sll1336 protein


Mass: 34576.434 Da / Num. of mol.: 1 / Fragment: N-terminal domain of ArgZ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll1336 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P74535
#2: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M KI, 0.1 M MES pH 6.5, 19% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.14→43.87 Å / Num. obs: 108732 / % possible obs: 99.4 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Rrim(I) all: 0.082 / Net I/σ(I): 13.1 / Num. measured all: 514396 / Scaling rejects: 453
Reflection shell

Diffraction-ID: 1 / % possible all: 99.2

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.14-1.164.60.5452472053190.8340.2770.6143
6.24-43.874.80.08333556920.9760.0430.09422.3

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
AMPLEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.14→43.87 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 1987 1.83 %
Rwork0.1733 106705 -
obs0.1737 108692 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.3 Å2 / Biso mean: 15.9112 Å2 / Biso min: 7.81 Å2
Refinement stepCycle: final / Resolution: 1.14→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 77 238 2498
Biso mean--24.04 26.24 -
Num. residues----273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.14-1.170.3831350.3527562769799
1.17-1.20.25861410.2727603774499
1.2-1.240.23331330.23277585771899
1.24-1.280.21881440.21497617776199
1.28-1.320.20721510.202675697720100
1.32-1.370.23221420.195576487790100
1.37-1.440.18721490.185976537802100
1.44-1.510.18641350.17357553768899
1.51-1.610.17211450.168976727817100
1.61-1.730.17451350.16476607795100
1.73-1.910.1741420.165676427784100
1.91-2.180.16961420.16497605774799
2.18-2.750.19331460.166676707816100
2.75-43.870.19121470.15667666781399

+
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