[English] 日本語
Yorodumi
- PDB-3a2y: E. coli Gsp amidase C59A complexed with Gsp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a2y
TitleE. coli Gsp amidase C59A complexed with Gsp
ComponentsBifunctional glutathionylspermidine synthetase/amidase
KeywordsHydrolase / Ligase / Gsp amidase / ATP-binding / Multifunctional enzyme / Nucleotide-binding
Function / homology
Function and homology information


glutathionylspermidine amidase / glutathionylspermidine synthase / glutathionylspermidine amidase activity / glutathionylspermidine synthase activity / spermidine metabolic process / glutathione metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutathionylspermidine synthase, pre-ATP-grasp-like domain / Glutathionylspermidine synthase preATP-grasp / CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Pre-ATP-grasp domain superfamily / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONYLSPERMIDINE / Bifunctional glutathionylspermidine synthetase/amidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPai, C.-H. / Ko, T.-P. / Chiang, B.-Y. / Lin, C.-H. / Wang, A.H.-J.
CitationJournal: Protein Sci. / Year: 2011
Title: Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases
Authors: Pai, C.-H. / Wu, H.-J. / Lin, C.-H. / Wang, A.H.-J.
History
DepositionJun 4, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Advisory / Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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 / 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 / _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: Bifunctional glutathionylspermidine synthetase/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6962
Polymers22,2621
Non-polymers4351
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bifunctional glutathionylspermidine synthetase/amidase
hetero molecules

A: Bifunctional glutathionylspermidine synthetase/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3934
Polymers44,5242
Non-polymers8692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area2360 Å2
ΔGint-7 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.962, 83.962, 104.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-3103-

HOH

21A-3107-

HOH

31A-3108-

HOH

-
Components

#1: Protein Bifunctional glutathionylspermidine synthetase/amidase / Glutathionylspermidine synthase / Glutathione:spermidine ligase [ADP-forming] / GSP synthetase / ...Glutathionylspermidine synthase / Glutathione:spermidine ligase [ADP-forming] / GSP synthetase / Glutathionylspermidine amidase / Glutathionylspermidine amidohydrolase [spermidine-forming] / GSP amidase


Mass: 22261.848 Da / Num. of mol.: 1 / Fragment: residues 1-197 / Mutation: C59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gsp, b2988, JW2956 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AES0, glutathionylspermidine synthase, glutathionylspermidine amidase
#2: Chemical ChemComp-TS5 / GLUTATHIONYLSPERMIDINE


Mass: 434.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M acetate, 0.8M NaH2PO4, 1.2M K2HPO4, 0.1M imidazole, pH 4.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 16593 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 61.9 / Num. measured all: 222956
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.9 / % possible all: 100

-
Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2iob

2iob


Resolution: 1.95→30 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 779 4.7 %random
Rwork0.2057 ---
all-16593 --
obs-15878 96.2 %-
Solvent computationBsol: 71.143 Å2
Displacement parametersBiso max: 96.21 Å2 / Biso mean: 43.635 Å2 / Biso min: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.384 Å2-0.925 Å20 Å2
2---0.384 Å20 Å2
3---0.768 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 29 131 1639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5991.5
X-RAY DIFFRACTIONc_scbond_it2.0962
X-RAY DIFFRACTIONc_mcangle_it2.6842
X-RAY DIFFRACTIONc_scangle_it3.3262.5
X-RAY DIFFRACTIONc_angle_deg1.2567
X-RAY DIFFRACTIONc_bond_d0.0062
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.3011 81 -
Rwork0.252 --
obs-1598 96.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3TS5_par.par

+
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