[English] 日本語
Yorodumi
- PDB-7qym: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-18... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qym
TitleStructure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-18 (R207V, D210P, S211W)
Components
  • Beta-aspartyl-peptidase
  • Isoaspartyl peptidase
KeywordsHYDROLASE / L-asparaginase / mutation
Function / homology
Function and homology information


beta-aspartyl-peptidase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity
Similarity search - Function
Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Beta-aspartyl-peptidase / Isoaspartyl peptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLoch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/38/E/NZ1/00035 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.
Authors: Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Gilski, M. / Jaskolski, M.
History
DepositionJan 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
AAA: Isoaspartyl peptidase
BBB: Beta-aspartyl-peptidase
CCC: Isoaspartyl peptidase
DDD: Beta-aspartyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,15311
Polymers66,9304
Non-polymers2237
Water11,061614
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-161 kcal/mol
Surface area20370 Å2
Unit cell
Length a, b, c (Å)49.552, 75.006, 146.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Isoaspartyl peptidase / Beta-aspartyl-peptidase / EcAIII / Isoaspartyl dipeptidase


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, beta-aspartyl-peptidase
#2: Protein Beta-aspartyl-peptidase


Mass: 14451.242 Da / Num. of mol.: 2 / Mutation: R207V, D210P, S211W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: iaaA, BH692_00390, EA435_03160, ELT72_09480, ELV13_05050, ELV22_03305, ELX56_08605, ELX68_03450, ELX70_05465, ELX79_08565, ELX83_03275, ELY23_01235, ELY24_20545, ELY50_10250, EPS76_07410, FNJ67_ ...Gene: iaaA, BH692_00390, EA435_03160, ELT72_09480, ELV13_05050, ELV22_03305, ELX56_08605, ELX68_03450, ELX70_05465, ELX79_08565, ELX83_03275, ELY23_01235, ELY24_20545, ELY50_10250, EPS76_07410, FNJ67_18185, G3565_10375, G6P89_17140, GRC73_03160, GUI33_12170, HIE29_000291
Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: A0A066T6R7, beta-aspartyl-peptidase
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 6K; 15% PEG 400; 0.2M MgCl2 in 0.1 Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.2→66.896 Å / Num. obs: 167749 / % possible obs: 98.1 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8018 / CC1/2: 0.556 / Rrim(I) all: 1.857 / % possible all: 95.7

-
Processing

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

2zal


Resolution: 1.2→66.896 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.638 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.032
RfactorNum. reflection% reflection
Rfree0.1534 1086 0.648 %
Rwork0.127 166598 -
all0.127 --
obs-167684 97.797 %
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: 19.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.915 Å20 Å20 Å2
2--1.462 Å2-0 Å2
3----3.377 Å2
Refinement stepCycle: LAST / Resolution: 1.2→66.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 7 614 4869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154406
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.636195
X-RAY DIFFRACTIONr_angle_other_deg1.6051.5710138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2221.912204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6751530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02992
X-RAY DIFFRACTIONr_nbd_refined0.2240.2936
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24377
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22167
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2389
X-RAY DIFFRACTIONr_metal_ion_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.220
X-RAY DIFFRACTIONr_nbd_other0.2960.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.241
X-RAY DIFFRACTIONr_mcbond_it2.1831.6712429
X-RAY DIFFRACTIONr_mcbond_other2.1721.672428
X-RAY DIFFRACTIONr_mcangle_it2.7382.5153046
X-RAY DIFFRACTIONr_mcangle_other2.7442.5153047
X-RAY DIFFRACTIONr_scbond_it3.7132.1062112
X-RAY DIFFRACTIONr_scbond_other3.7122.1072113
X-RAY DIFFRACTIONr_scangle_it4.0893.0113131
X-RAY DIFFRACTIONr_scangle_other4.0883.0123132
X-RAY DIFFRACTIONr_lrange_it4.67622.6975133
X-RAY DIFFRACTIONr_lrange_other4.61222.4125095
X-RAY DIFFRACTIONr_rigid_bond_restr3.30438947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.297650.25812015X-RAY DIFFRACTION95.6301
1.231-1.2650.266650.22511676X-RAY DIFFRACTION96.4908
1.265-1.3020.228750.20511461X-RAY DIFFRACTION96.6974
1.302-1.3420.189750.17911172X-RAY DIFFRACTION97.0322
1.342-1.3860.161750.16710790X-RAY DIFFRACTION97.0869
1.386-1.4340.186800.14910476X-RAY DIFFRACTION97.425
1.434-1.4880.146610.13310175X-RAY DIFFRACTION97.6159
1.488-1.5490.188570.1189876X-RAY DIFFRACTION97.7465
1.549-1.6180.161530.1049431X-RAY DIFFRACTION98.036
1.618-1.6970.12680.0999057X-RAY DIFFRACTION98.1922
1.697-1.7890.123600.0958636X-RAY DIFFRACTION98.4044
1.789-1.8970.135440.0928224X-RAY DIFFRACTION98.6282
1.897-2.0280.132530.17740X-RAY DIFFRACTION98.8082
2.028-2.190.139610.1067248X-RAY DIFFRACTION98.9709
2.19-2.3990.141510.1056703X-RAY DIFFRACTION99.2214
2.399-2.6820.13330.1096103X-RAY DIFFRACTION99.3041
2.682-3.0960.144430.125429X-RAY DIFFRACTION99.5271
3.096-3.790.16280.1294631X-RAY DIFFRACTION99.7004
3.79-5.3530.16280.1293634X-RAY DIFFRACTION99.7277
5.353-66.8960.16110.1982121X-RAY DIFFRACTION99.0246

+
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