[English] 日本語
Yorodumi
- PDB-5i4b: Erwinia chrysanthemi L-asparaginase E63Q +S254N mutation + L-Aspa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i4b
TitleErwinia chrysanthemi L-asparaginase E63Q +S254N mutation + L-Aspartic acid
ComponentsL-asparaginase
KeywordsHYDROLASE / L-asparaginase / Erwinia chrysanthemum / E63Q +S254N mutation / L-Aspartic acid
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytosol
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / 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. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / 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. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNguyen, H.A. / Lavie, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)RO1 EB013685 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Design and Characterization of Erwinia Chrysanthemi l-Asparaginase Variants with Diminished l-Glutaminase Activity.
Authors: Nguyen, H.A. / Su, Y. / Lavie, A.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: L-asparaginase
C: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3576
Polymers105,9583
Non-polymers3993
Water17,186954
1
A: L-asparaginase
hetero molecules

A: L-asparaginase
hetero molecules

A: L-asparaginase
hetero molecules

A: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8108
Polymers141,2774
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17380 Å2
ΔGint-41 kcal/mol
Surface area38260 Å2
MethodPISA
2
B: L-asparaginase
C: L-asparaginase
hetero molecules

B: L-asparaginase
C: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8108
Polymers141,2774
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17410 Å2
ΔGint-41 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.977, 123.124, 198.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

21A-762-

HOH

31B-788-

HOH

41C-741-

HOH

51C-780-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 3 - 327 / Label seq-ID: 4 - 328

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 35319.312 Da / Num. of mol.: 3 / Mutation: E63Q, S254N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Gene: ansB, asn / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P06608, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, pH 7.5 and 24% of PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.008264 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008264 Å / Relative weight: 1
ReflectionResolution: 1.6→104.62 Å / Num. obs: 122786 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.56 % / Biso Wilson estimate: 19.628 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.690.5573.36195.7
1.69-1.810.3715.13198.2
1.81-1.950.2298.03198.6
1.95-2.140.14612.04198.8
2.14-2.390.09617.21199.1
2.39-2.760.07321.59199.4
2.76-3.370.05327.6199.5
3.37-4.730.03835.41198.9
4.73-29.5020.03636.68196.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7J

1o7j


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.026 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 6005 5 %RANDOM
Rwork0.1542 ---
obs0.1557 114884 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.23 Å2 / Biso mean: 16.227 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 27 954 8325
Biso mean--16.42 26.66 -
Num. residues----975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197649
X-RAY DIFFRACTIONr_bond_other_d0.0110.027503
X-RAY DIFFRACTIONr_angle_refined_deg1.921.97110405
X-RAY DIFFRACTIONr_angle_other_deg1.559317211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27751008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82623.846312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1681557
X-RAY DIFFRACTIONr_chiral_restr0.120.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028818
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021675
X-RAY DIFFRACTIONr_mcbond_it1.7361.3973993
X-RAY DIFFRACTIONr_mcbond_other1.7351.3973992
X-RAY DIFFRACTIONr_mcangle_it2.5552.0915011
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A416620.05
12B416620.05
21A415720.06
22C415720.06
31B411980.06
32C411980.06
LS refinement shellResolution: 1.596→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 433 -
Rwork0.288 8143 -
all-8576 -
obs--93.79 %

+
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://pdbjlvh1.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