[English] 日本語
Yorodumi
- PDB-7r6b: Crystal structure of mutant R43D/L124D/R125A/C273S of L-Asparagin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r6b
TitleCrystal structure of mutant R43D/L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis
ComponentsL-asparaginase I
KeywordsHYDROLASE / L-ASPARAGINASE
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process / metal ion binding / cytosol
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile.
Similarity search - Domain/homology
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsStrzelczyk, P. / Wlodawer, A. / Lubkowski, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Febs J. / Year: 2023
Title: The dimeric form of bacterial l-asparaginase YpAI is fully active.
Authors: Strzelczyk, P. / Zhang, D. / Alexandratos, J. / Piszczek, G. / Wlodawer, A. / Lubkowski, J.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-asparaginase I
B: L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,08114
Polymers73,3812
Non-polymers70112
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-22 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.263, 115.893, 127.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 3 - 336 / Label seq-ID: 3 - 336

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein L-asparaginase I


Mass: 36690.309 Da / Num. of mol.: 2 / Mutation: R43D, L124D, R125A, C273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ansA, YPO2161 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A3N4B0Q2, asparaginase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.2 M Calcium acetate, 10% (w/v) PEG 8000, 0.1 M Imidazole/ Hydrochloric acid, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2020
RadiationMonochromator: Double crystal - liquid nitrogen cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 47794 / % possible obs: 98.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Net I/σ(I): 22
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2370 / CC1/2: 0.719 / Rpim(I) all: 0.47 / % possible all: 99.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTX

3ntx


Resolution: 2.03→48.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.234 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2372 5.1 %RANDOM
Rwork0.1699 ---
obs0.1724 44242 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.19 Å2 / Biso mean: 31.099 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2--0.14 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2.03→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 42 383 5071
Biso mean--54.63 40.35 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134791
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174473
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.6376496
X-RAY DIFFRACTIONr_angle_other_deg1.4811.56410395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9895595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17424235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36515788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9411520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025289
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02899
Refine LS restraints NCS

Ens-ID: 1 / Number: 8892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.03→2.08 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 130 -
Rwork0.256 2670 -
obs--78.63 %

+
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