[English] 日本語
Yorodumi
- PDB-7esr: Crystal structure of Synechocystis sp PCC6803 guanidinium hydrola... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7esr
TitleCrystal structure of Synechocystis sp PCC6803 guanidinium hydrolase (R32)
ComponentsProbable agmatinase 2
KeywordsHYDROLASE / ureohydrolase family protein / arginase/agmatinase family protein / Ni2+ enzyme / 2-metal ion cluster / METAL BINDING PROTEIN
Function / homology
Function and homology information


agmatinase / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding
Similarity search - Function
Agmatinase-related / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Probable agmatinase 2
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMayans, O.M. / Fleming, J.R.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)681777 Germany
CitationJournal: Nature / Year: 2022
Title: Discovery of a Ni 2+ -dependent guanidine hydrolase in bacteria.
Authors: Funck, D. / Sinn, M. / Fleming, J.R. / Stanoppi, M. / Dietrich, J. / Lopez-Igual, R. / Mayans, O. / Hartig, J.S.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 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: Probable agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4016
Polymers43,1381
Non-polymers2635
Water5,855325
1
A: Probable agmatinase 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)260,40736
Polymers258,8276
Non-polymers1,58030
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area46110 Å2
ΔGint-332 kcal/mol
Surface area56440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.700, 140.700, 95.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-623-

HOH

31A-657-

HOH

41A-709-

HOH

51A-922-

HOH

61A-923-

HOH

-
Components

#1: Protein Probable agmatinase 2 / guanidine hydrolase / Agmatine ureohydrolase 2 / AUH 2


Mass: 43137.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P73270, agmatinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.06 M (0.3M magnesium chloride hexahydrate, 0.3M calcium chloride dehydrate), 0.1M (1M HEPES; MOPS) pH7.5, 30 % [v/v] (40% [v/v] ethylene glycol, 20% [w/v] PEG 8000)

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→28.97 Å / Num. obs: 67577 / % possible obs: 99.03 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.24
Reflection shellResolution: 1.42→1.43 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1320 / CC1/2: 0.515

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NIO

3nio


Resolution: 1.42→28.97 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1476 2026 3 %
Rwork0.1317 65502 -
obs0.1322 67528 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.42→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 14 325 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783022
X-RAY DIFFRACTIONf_angle_d1.00744114
X-RAY DIFFRACTIONf_chiral_restr0.0838462
X-RAY DIFFRACTIONf_plane_restr0.0125540
X-RAY DIFFRACTIONf_dihedral_angle_d13.78781117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.53851310.56764289X-RAY DIFFRACTION91.15
1.45-1.490.37291350.38324537X-RAY DIFFRACTION96.97
1.49-1.540.27371540.23834654X-RAY DIFFRACTION99.75
1.54-1.590.20721460.18254727X-RAY DIFFRACTION99.86
1.59-1.640.18261410.16774676X-RAY DIFFRACTION99.92
1.64-1.710.17111300.15534721X-RAY DIFFRACTION99.94
1.71-1.790.16261390.144687X-RAY DIFFRACTION99.96
1.79-1.880.15331550.12164703X-RAY DIFFRACTION99.67
1.88-20.13061630.10964689X-RAY DIFFRACTION99.9
2-2.150.13541550.10564726X-RAY DIFFRACTION99.94
2.15-2.370.10841410.10384711X-RAY DIFFRACTION100
2.37-2.710.11931570.114738X-RAY DIFFRACTION99.71
2.71-3.420.13111230.11274776X-RAY DIFFRACTION99.98
3.42-28.970.14721560.13254868X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: -2.38772611308 Å / Origin y: 22.083574978 Å / Origin z: 16.9110270252 Å
111213212223313233
T0.258729180738 Å20.00843531641217 Å20.0193171545241 Å2-0.194165299095 Å2-0.0293811805589 Å2--0.224638873946 Å2
L0.339457954139 °2-0.0562730271783 °20.0878028838993 °2-0.211379301423 °2-0.0171939612654 °2--0.501229659144 °2
S0.00407398972877 Å °-0.0717736016072 Å °0.103407023063 Å °0.0715845361783 Å °0.0183402010039 Å °-0.0044967133708 Å °-0.173456396425 Å °-0.0197531095409 Å °-1.71003487009E-6 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 601)

+
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