[English] 日本語
Yorodumi
- PDB-8bqo: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant M200I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bqo
TitleStructure of E.coli Class 2 L-asparaginase EcAIII, mutant M200I
Components(Isoaspartyl peptidase subunit ...) x 2
KeywordsHYDROLASE / L-asparaginase / isoaspartylpeptidase / mutation / Ntn-hydrolase
Function / homologybeta-aspartyl-peptidase / Peptidase T2, asparaginase 2 / Asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Isoaspartyl peptidase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSciuk, A. / Ruszkowski, M. / Jaskolski, M. / Loch, J.I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/38/E/NZ1/00035 Poland
CitationJournal: Protein Sci. / Year: 2023
Title: The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII.
Authors: Janicki, M. / Sciuk, A. / Zielezinski, A. / Ruszkowski, M. / Ludwikow, A. / Karlowski, W.M. / Jaskolski, M. / Loch, J.I.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Isoaspartyl peptidase subunit alpha
BBB: Isoaspartyl peptidase subunit beta
CCC: Isoaspartyl peptidase subunit alpha
DDD: Isoaspartyl peptidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1139
Polymers66,8484
Non-polymers2665
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-119 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.923, 77.671, 148.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Isoaspartyl peptidase subunit ... , 2 types, 4 molecules AAACCCBBBDDD

#1: Protein Isoaspartyl peptidase subunit alpha


Mass: 19013.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595
#2: Protein Isoaspartyl peptidase subunit beta


Mass: 14410.107 Da / Num. of mol.: 2 / Mutation: M200I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595

-
Non-polymers , 4 types, 239 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20-30% PEG4000,10-15% PEG400, 0.2M MgCl2 in 100mM Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17.21 Å / Num. obs: 35616 / % possible obs: 97.9 % / Redundancy: 2.9 % / CC1/2: 0.983 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.169 / Net I/σ(I): 5.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2887 / CC1/2: 0.514 / Rrim(I) all: 0.838 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZAL

2zal


Resolution: 2.1→17.209 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.328 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.179
RfactorNum. reflection% reflection
Rfree0.2315 1064 2.991 %
Rwork0.1823 34515 -
all0.184 --
obs-35579 97.453 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.123 Å20 Å20 Å2
2---0.273 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 15 234 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154176
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.635885
X-RAY DIFFRACTIONr_angle_other_deg1.3541.5719582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8965590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.49421.94201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
X-RAY DIFFRACTIONr_nbd_refined0.2090.2906
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.24200
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22141
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.214
X-RAY DIFFRACTIONr_nbd_other0.2250.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.29
X-RAY DIFFRACTIONr_mcbond_it1.2541.8112345
X-RAY DIFFRACTIONr_mcbond_other1.2531.812344
X-RAY DIFFRACTIONr_mcangle_it1.9842.7082928
X-RAY DIFFRACTIONr_mcangle_other1.9842.7092929
X-RAY DIFFRACTIONr_scbond_it1.8112.1221996
X-RAY DIFFRACTIONr_scbond_other1.812.1231997
X-RAY DIFFRACTIONr_scangle_it2.8963.0782953
X-RAY DIFFRACTIONr_scangle_other2.8953.0792954
X-RAY DIFFRACTIONr_lrange_it4.17222.5124781
X-RAY DIFFRACTIONr_lrange_other4.14422.474761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.232750.2272537X-RAY DIFFRACTION98.6032
2.155-2.2140.299650.2282499X-RAY DIFFRACTION99.0726
2.214-2.2780.309710.2052438X-RAY DIFFRACTION99.6426
2.278-2.3480.282800.2132358X-RAY DIFFRACTION99.6322
2.348-2.4250.23730.1992304X-RAY DIFFRACTION99.6646
2.425-2.510.259690.192228X-RAY DIFFRACTION99.6097
2.51-2.6040.174690.1882131X-RAY DIFFRACTION99.8185
2.604-2.710.276740.1922052X-RAY DIFFRACTION99.5318
2.71-2.8310.225770.1931976X-RAY DIFFRACTION99.2747
2.831-2.9690.249610.1781925X-RAY DIFFRACTION99.3497
2.969-3.1290.292530.1781805X-RAY DIFFRACTION98.935
3.129-3.3180.178460.1711699X-RAY DIFFRACTION97.8139
3.318-3.5470.248350.1811569X-RAY DIFFRACTION95.0237
3.547-3.830.189400.161438X-RAY DIFFRACTION94.0204
3.83-4.1950.229380.1451278X-RAY DIFFRACTION90.2606
4.195-4.6880.204450.1431138X-RAY DIFFRACTION88.9474
4.688-5.410.219320.1641048X-RAY DIFFRACTION91.9149
5.41-6.6170.26230.196958X-RAY DIFFRACTION95.614
6.617-9.3210.145260.151768X-RAY DIFFRACTION98.2673
9.321-17.2090.139120.193366X-RAY DIFFRACTION77.1429

+
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