[English] 日本語
Yorodumi
- PDB-5ns1: Cys-Gly dipeptidase GliJ in complex with Ni2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ns1
TitleCys-Gly dipeptidase GliJ in complex with Ni2+
ComponentsDipeptidase gliJ
KeywordsHYDROLASE / carboxypeptidase / dipeptidase / gliotoxin biosynthesis
Function / homology
Function and homology information


symbiont-mediated suppression of host immune response / gliotoxin biosynthetic process / membrane dipeptidase / mycotoxin biosynthetic process / metallodipeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Dipeptidase gliJ
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
Hans-Fischer-Gesellschaft Germany
German Research FoundationSFB749 Germany
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ.
Authors: Marion, A. / Groll, M. / Scharf, D.H. / Scherlach, K. / Glaser, M. / Sievers, H. / Schuster, M. / Hertweck, C. / Brakhage, A.A. / Antes, I. / Huber, E.M.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dipeptidase gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1614
Polymers45,0081
Non-polymers1533
Water1,36976
1
A: Dipeptidase gliJ
hetero molecules

A: Dipeptidase gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3228
Polymers90,0162
Non-polymers3066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area7200 Å2
ΔGint-98 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.350, 99.350, 107.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Dipeptidase gliJ / Gliotoxin biosynthesis protein J


Mass: 45008.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: gliJ, AFUA_6G09650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WMJ8, membrane dipeptidase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 5% isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.48432 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48432 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 46316 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LX0

5lx0


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 14.003 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20052 1214 5 %RANDOM
Rwork0.18426 ---
obs0.18508 23080 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å2-0 Å2
2--0.56 Å20 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 3 76 3086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193063
X-RAY DIFFRACTIONr_bond_other_d0.0010.022861
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9534142
X-RAY DIFFRACTIONr_angle_other_deg0.89536599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2525380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97123.117154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7961533
X-RAY DIFFRACTIONr_chiral_restr0.0560.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2786.1781523
X-RAY DIFFRACTIONr_mcbond_other1.2786.1751522
X-RAY DIFFRACTIONr_mcangle_it1.3669.2551902
X-RAY DIFFRACTIONr_mcangle_other1.3669.2581903
X-RAY DIFFRACTIONr_scbond_it1.5456.6441540
X-RAY DIFFRACTIONr_scbond_other1.5446.6451541
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.539.7822241
X-RAY DIFFRACTIONr_long_range_B_refined2.04471.8613258
X-RAY DIFFRACTIONr_long_range_B_other2.02771.7913252
X-RAY DIFFRACTIONr_rigid_bond_restr0.35935921
X-RAY DIFFRACTIONr_sphericity_free29.146561
X-RAY DIFFRACTIONr_sphericity_bonded6.09455886
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 87 -
Rwork0.291 1654 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -14.1133 Å / Origin y: 68.8651 Å / Origin z: 16.6412 Å
111213212223313233
T0.0729 Å2-0.0413 Å20.0019 Å2-0.1123 Å20.0123 Å2--0.0048 Å2
L0.0127 °2-0.0628 °20.0044 °2-0.8725 °20.0631 °2--0.1268 °2
S-0.0218 Å °0.0135 Å °-0.0044 Å °0.0156 Å °0.0406 Å °0.0297 Å °0.0428 Å °-0.0397 Å °-0.0188 Å °

+
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