[English] 日本語
Yorodumi
- PDB-8rug: Crystal structure of Rhizobium etli L-asparaginase ReAV C189A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rug
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV C189A mutant
ComponentsL-asparaginase II protein
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / l-asparaginases / zinc-binding proteins / site-directed mutagenesis
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / DI(HYDROXYETHYL)ETHER / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPokrywka, K. / Grzechowiak, M. / Sliwiak, J. / Worsztynowicz, P. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
Citation
Journal: Front Chem / Year: 2024
Title: Probing the active site of Class 3 L-asparaginase by mutagenesis. I. Tinkering with the zinc coordination site of ReAV.
Authors: Pokrywka, K. / Grzechowiak, M. / Sliwiak, J. / Worsztynowicz, P. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
#1: Journal: IUCrJ / Year: 2021
Title: Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity.
Authors: Loch, J.I. / Jaskolski, M.
#2: 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.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center.
Authors: Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Grzechowiak, M. / Imiolczyk, B. / Pokrywka, K. / Chwastyk, M. / Gilski, M. / Jaskolski, M.
History
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-asparaginase II protein
B: L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,16317
Polymers79,0462
Non-polymers1,11715
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-21 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.046, 91.292, 105.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein L-asparaginase II protein


Mass: 39522.805 Da / Num. of mol.: 2 / Mutation: C189A
Source method: isolated from a genetically manipulated source
Details: point mutation C189A / Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: ansA, RHE_PE00350 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2K0Z2

-
Non-polymers , 5 types, 710 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 8000, 0.2 M Li2SO4, 0.1 M Bicine pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→78.05 Å / Num. obs: 83283 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.158 / Net I/σ(I): 14.95
Reflection shellResolution: 1.7→1.81 Å / Rmerge(I) obs: 1.649 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 13254 / CC1/2: 0.665 / Rrim(I) all: 1.721

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→69.09 Å / SU ML: 0.1888 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hydrogen atoms were added at riding position.
RfactorNum. reflection% reflection
Rfree0.1857 999 1.2 %
Rwork0.1623 82260 -
obs0.1625 83259 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 70 695 6091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01015695
X-RAY DIFFRACTIONf_angle_d1.05837723
X-RAY DIFFRACTIONf_chiral_restr0.0684861
X-RAY DIFFRACTIONf_plane_restr0.01061024
X-RAY DIFFRACTIONf_dihedral_angle_d13.25212156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.29211400.273711571X-RAY DIFFRACTION99.61
1.79-1.90.22761420.199611665X-RAY DIFFRACTION100
1.9-2.050.23951410.184811629X-RAY DIFFRACTION99.99
2.05-2.260.16351420.150611666X-RAY DIFFRACTION99.98
2.26-2.580.21430.159211749X-RAY DIFFRACTION99.98
2.58-3.260.19951440.159711825X-RAY DIFFRACTION99.97
3.26-69.090.15151470.142512155X-RAY DIFFRACTION99.85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.335963808850.575192707449-0.3585919085521.271248533930.03271361148661.052519718960.0161335104571-0.00687705512620.162964897880.0376423985284-0.006150863002350.17693492477-0.100122953005-0.2162211066340.003989296582770.09838654651970.01116380584940.003503640403340.152373856914-0.01591387041940.1538248423791.755869775595.1177046056827.9423073458
20.5938553382160.4074308622580.1042929890691.063745072940.1965304284320.5834438296150.0430643270812-0.05000910315540.02184802476380.0949267928256-0.05276752183320.0108509838515-0.04513053714180.03287897017230.01183412669440.128829042205-0.01017871939390.01225799696820.1311241788620.01449370780940.13813120064234.200282703611.295357429531.6338070521
33.429201076231.98786450902-1.713421733442.76668601441-2.152475975082.412436007430.36013526959-0.228814256603-0.07876776859190.710307006106-0.2514604781610.354455755089-0.0843493695225-0.118949883647-0.09533008574330.279115329858-0.07568631221410.05906003912590.186992929948-0.02121541838470.17249298715529.341592585215.919131959146.8661148751
41.540286662680.09110967495040.0649113250361.920964971890.1821338784621.138404745290.0132328529698-0.04737367075780.103782587780.0495782220493-0.0207219153523-0.0651642161701-0.0883003157140.06182973865230.006685746458030.122769331738-0.03524208861790.0152523559740.103477540838-0.0002624294740080.12128828744440.252079291221.27346004628.3846136584
51.575029699240.605596075389-0.1112487477281.413028083870.3644270246881.309178835580.0258444623098-0.0573098958099-0.1905617672680.131018048098-0.0122047718026-0.2218097022070.1436077940710.152397158568-0.0007742942082060.1176090204520.00609079699325-0.007541200322560.1040948891830.01734631456620.14670247756239.69255350331.0566207785229.5246153603
61.717924372721.61371757702-2.34539378132.5593890819-3.498788745437.08208633304-0.04348094587760.0422913749911-0.105582394704-0.0761840947709-0.0418139868018-0.04293004285850.06117207543420.1124583697710.1513125157070.1232282038110.0133043999040.0008434373378560.0933546227309-0.01371007916580.15504370640828.9468314559-7.5322640580119.499872353
76.099652087723.243430493421.378565321912.437624868670.6667792648571.30574042072-0.1585867202990.3287059076790.00444745604664-0.2447887481220.1082073014830.036874032881-0.0959761522948-0.05496952907470.06237942640350.1232042821050.00621633645731-0.001365517681920.145231799159-0.007364951757060.1250530561513.2688579616.1531625334818.7981912024
80.4919310267880.0584211465694-0.2695358657920.577400721793-0.1552831925080.793260083482-0.0162827294557-0.00354441109185-0.05820655538920.0938220471449-0.03294699615460.127766698120.106818439643-0.1547286344020.04044074443010.163418497875-0.04869726382090.02135025900870.169456643539-0.03817031459940.154854868297-0.502126205804-12.277698199634.9529187338
92.449393921472.650121567471.51703535235.36884968312.247557258281.676534082280.122715815432-0.0872902396077-0.1403927233880.119103780649-0.0492572783635-0.1897840084170.156668908043-0.01780689988-0.07740504554950.188031058524-0.03077571313140.0367972259140.163293811447-0.005073006269490.130098946238.12065719901-15.93956617145.5632063424
101.97287273595-0.5495954899631.068463550781.69834409713-0.7175364298591.37309528448-0.0001355584146960.0275374475087-0.0403510533521-0.110174755664-0.0304337024830.1095834150920.25033145683-0.2246182688640.03667469533030.166404810717-0.08081696181910.01601023629330.186541946126-0.03912553072030.1376731169390.917370127944-16.916281662825.3142028099
112.700635678332.32397393190.5408442529748.22214666966-0.165566612880.193220577721-0.1620465366390.4112069819740.00226221693843-0.22809184276-0.1807628387390.8711619265610.10443007335-0.9119339831910.2096975337450.193111735967-0.1076121371530.0433624071610.497382100151-0.07437581023620.279755929432-12.910589069-12.275285067131.5203000905
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 238 through 352 )BJ238 - 352237 - 351
22chain 'A' and (resid -3 through 114 )AA-3 - 1141 - 118
33chain 'A' and (resid 115 through 149 )AA115 - 149119 - 153
44chain 'A' and (resid 150 through 237 )AA150 - 237154 - 241
55chain 'A' and (resid 238 through 329 )AA238 - 329242 - 333
66chain 'A' and (resid 330 through 367 )AA330 - 367334 - 368
77chain 'B' and (resid 2 through 28 )BJ2 - 281 - 27
88chain 'B' and (resid 29 through 97 )BJ29 - 9728 - 96
99chain 'B' and (resid 98 through 161 )BJ98 - 16197 - 160
1010chain 'B' and (resid 162 through 217 )BJ162 - 217161 - 216
1111chain 'B' and (resid 218 through 237 )BJ218 - 237217 - 236

+
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