[English] 日本語
Yorodumi
- PDB-7os5: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7os5
TitleCrystal structure of Rhizobium etli inducible L-asparaginase ReAV (orthorhombic form OP)
ComponentsL-asparaginase
KeywordsHYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.293 Å
AuthorsLoch, J.I. / Imiolczyk, B. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
Citation
Journal: Nat Commun / Year: 2021
Title: Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site.
Authors: Loch, J.I. / Imiolczyk, B. / Sliwiak, J. / Wantuch, A. / Bejger, M. / Gilski, M. / Jaskolski, M.
#1: Journal: Acta Biochim Pol / Year: 2001
Title: Sequence analysis of enzymes with asparaginase activity
Authors: Borek, D. / Jaskolski, M.
History
DepositionJun 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 26, 2023Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Feb 7, 2024Group: 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
AAA: L-asparaginase
BBB: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,39317
Polymers79,1422
Non-polymers1,25115
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-230 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.231, 91.142, 106.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 4 - 351 / Label seq-ID: 10 - 357

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein L-asparaginase


Mass: 39570.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Class 3 (R. etli) type L-asparaginase
Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria)
Strain: CFN 42 / ATCC 51251 / Gene: ansA, RHE_PE00350 / Plasmid: pET151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2K0Z2

-
Non-polymers , 5 types, 643 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.29→69.11 Å / Num. obs: 131038 / % possible obs: 95.4 % / Redundancy: 12.7 % / Biso Wilson estimate: 19.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Rrim(I) all: 0.179 / Net I/σ(I): 10.4
Reflection shellResolution: 1.29→1.4 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.008 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6526 / CC1/2: 0.4 / Rpim(I) all: 0.639 / Rrim(I) all: 2.113 / % possible all: 64.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OS3

7os3


Resolution: 1.293→69.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.326 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1000 0.771 %RANDOM
Rwork0.1547 128695 --
all0.155 ---
obs-129695 68.626 %-
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: 13.957 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.012 Å2-0 Å2
3----1.002 Å2
Refinement stepCycle: LAST / Resolution: 1.293→69.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 61 628 5992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135539
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175207
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6177514
X-RAY DIFFRACTIONr_angle_other_deg1.5541.58111990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22720.246284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40415898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971554
X-RAY DIFFRACTIONr_chiral_restr0.090.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021255
X-RAY DIFFRACTIONr_nbd_refined0.2130.21163
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.24850
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22710
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2455
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.219
X-RAY DIFFRACTIONr_nbd_other0.2020.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.221
X-RAY DIFFRACTIONr_mcbond_it1.8221.1482902
X-RAY DIFFRACTIONr_mcbond_other1.8141.1472900
X-RAY DIFFRACTIONr_mcangle_it2.3251.7313635
X-RAY DIFFRACTIONr_mcangle_other2.3241.7313635
X-RAY DIFFRACTIONr_scbond_it3.261.5492637
X-RAY DIFFRACTIONr_scbond_other3.161.5332614
X-RAY DIFFRACTIONr_scangle_it3.8692.1893864
X-RAY DIFFRACTIONr_scangle_other3.7482.1613829
X-RAY DIFFRACTIONr_lrange_it4.52215.9666288
X-RAY DIFFRACTIONr_lrange_other4.34515.6686228
X-RAY DIFFRACTIONr_rigid_bond_restr6.399310746
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0511159
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.081240.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.081240.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.293-1.3260.31180.25812850.258138200.8250.9119.3560.224
1.326-1.3630.29390.25317580.253134950.8820.89713.09370.249
1.363-1.4020.234200.25332290.253131460.8590.87224.71470.246
1.402-1.4450.301400.23248030.232128060.8040.86337.81820.225
1.445-1.4930.262460.22961790.229123330.8390.8650.47430.22
1.493-1.5450.307480.23274720.232119940.8480.85762.6980.211
1.545-1.6030.269630.20480960.204116180.8710.8970.22720.18
1.603-1.6690.221860.18489200.185111330.90.91680.89460.156
1.669-1.7430.21690.17797090.177107060.8970.92591.3320.14
1.743-1.8280.247810.175101240.176102380.9170.92699.67770.131
1.828-1.9270.203830.14596620.14697450.9320.9441000.119
1.927-2.0440.19610.12591720.12592340.9610.95999.98920.11
2.044-2.1850.157710.11986520.11987260.9670.96699.96560.111
2.185-2.3590.156610.11680580.11681320.9620.97199.84010.111
2.359-2.5840.21650.11974280.1274960.9570.97299.960.118
2.584-2.8890.152420.13767390.13767830.9640.96499.97050.141
2.889-3.3350.159460.14959910.14960500.9660.96299.78510.161
3.335-4.0820.188480.14150870.14251370.9640.97499.96110.158
4.082-5.7620.193330.14740030.14840420.9680.97499.85160.177
5.762-69.1130.135200.20323280.20223550.9850.95799.70280.239

+
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