[English] 日本語
Yorodumi
- PDB-4g1p: Structural and Mechanistic Basis of Substrate Recognition by Nove... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g1p
TitleStructural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccharomyces cerevisiae
ComponentsCys-Gly metallodipeptidase DUG1
KeywordsHYDROLASE / Di-nuclear peptidases / M20 family metallo-peptidases / alpha/beta scaffold / N-terminal catalytic domain/C-terminal lid domain
Function / homology
Function and homology information


Glutathione synthesis and recycling / Paracetamol ADME / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / glutathione catabolic process / metallodipeptidase activity / peptidase activity / omega peptidase activity / mitochondrion / proteolysis / metal ion binding ...Glutathione synthesis and recycling / Paracetamol ADME / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / glutathione catabolic process / metallodipeptidase activity / peptidase activity / omega peptidase activity / mitochondrion / proteolysis / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Cytosolic nonspecific dipeptidase/DUG1 / : / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Cytosolic nonspecific dipeptidase/DUG1 / : / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / GLYCINE / Cys-Gly metallodipeptidase DUG1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.547 Å
AuthorsSingh, A.K. / Singh, M. / Pandya, V.K. / Singh, V. / Mittal, M. / Kumaran, S.
CitationJournal: To be published
Title: Structural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccromyces cerevesiae
Authors: Singh, A.K. / Singh, M. / Pandya, V.K. / Singh, V. / Mittal, M. / Kumaran, S.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Other
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cys-Gly metallodipeptidase DUG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0875
Polymers53,7601
Non-polymers3274
Water3,027168
1
A: Cys-Gly metallodipeptidase DUG1
hetero molecules

A: Cys-Gly metallodipeptidase DUG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,17410
Polymers107,5202
Non-polymers6548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area7290 Å2
ΔGint-127 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.132, 119.132, 176.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Cys-Gly metallodipeptidase DUG1 / Deficient in utilization of glutathione protein 1 / GSH degradosomal complex subunit DUG1


Mass: 53760.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: Dug1p / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P43616, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDI-PEPTIDE, GLY-CYS IS INTRINSIC DIPEPTIDE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M AmSO4, 0.1 M tri-Na citrate pH 5.6, 1.0 M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.547→50 Å / Num. obs: 24507 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 36.42 Å2 / Rmerge(I) obs: 0.216
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 11.21 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.27

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZOF

2zof


Resolution: 2.547→19.731 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.841 / SU ML: 0.32 / σ(F): 1.99 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1225 5 %random
Rwork0.1859 ---
obs0.1881 24487 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.74 Å2 / Biso mean: 36.42 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: LAST / Resolution: 2.547→19.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 12 168 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083791
X-RAY DIFFRACTIONf_angle_d1.1355125
X-RAY DIFFRACTIONf_chiral_restr0.072573
X-RAY DIFFRACTIONf_plane_restr0.006657
X-RAY DIFFRACTIONf_dihedral_angle_d14.7341402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5474-2.64920.29811310.25822487261897
2.6492-2.76950.3111350.23625612696100
2.7695-2.9150.27441350.210925592694100
2.915-3.0970.23761350.197525602695100
3.097-3.33510.24941360.184925872723100
3.3351-3.66880.27511330.20542523265697
3.6688-4.19520.21841330.17952543267697
4.1952-5.26880.16341400.140626572797100
5.2688-19.73120.19791470.16912785293299

+
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