[English] 日本語
Yorodumi
- PDB-6juy: Crystal Structure of ArgZ, apo structure, an Arginine Dihydrolase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6juy
TitleCrystal Structure of ArgZ, apo structure, an Arginine Dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria
ComponentsSll1336 protein
KeywordsHYDROLASE / arginine dihydrolase / amidino-transferase domain / alpha/beta propeller fold / LOR/SDH superfamily
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 / Arginine deiminase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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 1.3Nov 22, 2023Group: 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: Sll1336 protein
B: Sll1336 protein
C: Sll1336 protein
D: Sll1336 protein


Theoretical massNumber of molelcules
Total (without water)314,1754
Polymers314,1754
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-62 kcal/mol
Surface area98760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.865, 105.439, 165.905
Angle α, β, γ (deg.)90.000, 113.180, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 6 and (name N...
21(chain B and ((resid 4 through 6 and (name N...
31(chain C and (resid 4 through 12 or (resid 34...
41(chain D and ((resid 4 through 6 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 4 through 6 and (name N...A0
211(chain B and ((resid 4 through 6 and (name N...B0
311(chain C and (resid 4 through 12 or (resid 34...C0
411(chain D and ((resid 4 through 6 and (name N...D4 - 6
421(chain D and ((resid 4 through 6 and (name N...D3 - 696
431(chain D and ((resid 4 through 6 and (name N...D3 - 696
441(chain D and ((resid 4 through 6 and (name N...D3 - 696
451(chain D and ((resid 4 through 6 and (name N...D3 - 696

-
Components

#1: Protein
Sll1336 protein


Mass: 78543.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll1336 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P74535
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.24 M ammonium formate, 17% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.97→48.74 Å / Num. obs: 60551 / % possible obs: 97.3 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 18.4 / Num. measured all: 263617 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.97-3.054.50.5642054045240.8660.2920.637299
13.28-48.744.20.02429467040.9990.0130.02842.795.1

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2Q, 3MGJ, 6JV0

3c2q

3mgj

6jv0


Resolution: 2.97→41.06 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1987 3.28 %
Rwork0.2341 58522 -
obs0.2354 60509 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.72 Å2 / Biso mean: 109.3208 Å2 / Biso min: 58.32 Å2
Refinement stepCycle: final / Resolution: 2.97→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18514 0 0 5 18519
Biso mean---78.98 -
Num. residues----2555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9856X-RAY DIFFRACTION17.734TORSIONAL
12B9856X-RAY DIFFRACTION17.734TORSIONAL
13C9856X-RAY DIFFRACTION17.734TORSIONAL
14D9856X-RAY DIFFRACTION17.734TORSIONAL
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 (%)
2.97-3.040.39161500.3674211436199
3.04-3.130.34461430.32594260440399
3.13-3.220.32781430.28794187433098
3.22-3.320.33751510.28434183433498
3.32-3.440.35321250.28934011413694
3.44-3.580.37791420.2894116425895
3.58-3.740.33171480.2684219436799
3.74-3.940.31991370.26154238437599
3.94-4.190.28131440.24284236438098
4.19-4.510.26051430.21654183432698
4.51-4.960.25181340.21164160429496
4.96-5.680.28411400.23744065420594
5.68-7.150.30441420.2524285442799
7.15-41.060.20011450.18574168431394

+
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