[English] 日本語
Yorodumi
- PDB-6v5f: L-asparaginase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v5f
TitleL-asparaginase from Escherichia coli
ComponentsL-asparaginase 2Asparaginase
KeywordsHYDROLASE / L-asparaginase / catalytic mechanism / leukemia
Function / homology
Function and homology information


asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
Similarity search - Function
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, 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.
Similarity search - Domain/homology
ASPARTIC ACID / SUCCINIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSouza, T.A.C.B. / Morais, S.B. / Morini, F.S. / Meissner, G.O.
CitationJournal: To Be Published
Title: L-asparaginase from Escherichia coli: Novel insights about the behavior of flexible part of the active site
Authors: Souza, T.A.C.B. / Morais, S.B. / Morini, F.S. / Meissner, G.O.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0108
Polymers138,5074
Non-polymers5024
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-43 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.917, 125.435, 68.816
Angle α, β, γ (deg.)90.000, 106.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 10 or resid 45...
21(chain B and (resid 1 through 10 or resid 45...
31(chain C and (resid 1 through 10 or resid 45...
41(chain D and (resid 1 through 10 or resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 10 or resid 45...A1 - 10
121(chain A and (resid 1 through 10 or resid 45...A45 - 77
131(chain A and (resid 1 through 10 or resid 45...A79 - 184
141(chain A and (resid 1 through 10 or resid 45...A186 - 195
151(chain A and (resid 1 through 10 or resid 45...A1 - 326
161(chain A and (resid 1 through 10 or resid 45...A265 - 280
171(chain A and (resid 1 through 10 or resid 45...A289 - 325
211(chain B and (resid 1 through 10 or resid 45...B1 - 10
221(chain B and (resid 1 through 10 or resid 45...B45 - 48
231(chain B and (resid 1 through 10 or resid 45...B50 - 18
241(chain B and (resid 1 through 10 or resid 45...B1 - 326
251(chain B and (resid 1 through 10 or resid 45...B265 - 280
261(chain B and (resid 1 through 10 or resid 45...B265 - 280
271(chain B and (resid 1 through 10 or resid 45...B289 - 325
311(chain C and (resid 1 through 10 or resid 45...C1 - 10
321(chain C and (resid 1 through 10 or resid 45...C45 - 48
331(chain C and (resid 1 through 10 or resid 45...C50 - 77
341(chain C and (resid 1 through 10 or resid 45...C79 - 184
351(chain C and (resid 1 through 10 or resid 45...C186 - 280
361(chain C and (resid 1 through 10 or resid 45...C289 - 325
411(chain D and (resid 1 through 10 or resid 45...D1 - 10
421(chain D and (resid 1 through 10 or resid 45...D45 - 48
431(chain D and (resid 1 through 10 or resid 45...D50 - 77
441(chain D and (resid 1 through 10 or resid 45...D79 - 195
451(chain D and (resid 1 through 10 or resid 45...D197 - 263
461(chain D and (resid 1 through 10 or resid 45...D265 - 325

-
Components

#1: Protein
L-asparaginase 2 / Asparaginase / L-asparaginase II / L-ASNase II / L-asparagine amidohydrolase II


Mass: 34626.809 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00805, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M succinic acid pH 7.0, 15% (w/v) polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 105403 / % possible obs: 97.7 % / Redundancy: 3.15 % / Biso Wilson estimate: 48.634 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.199 / Χ2: 1.496 / Net I/σ(I): 5.38
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.413 % / Mean I/σ(I) obs: 0.33 / Num. unique obs: 16633 / CC1/2: 0.214 / Rrim(I) all: 3.401 / % possible all: 95.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å33.37 Å
Translation2.2 Å33.37 Å

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eca

3eca


Resolution: 2.1→33.37 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2976 1976 3.87 %
Rwork0.2298 49025 -
obs0.2325 51001 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.13 Å2 / Biso mean: 43.543 Å2 / Biso min: 21.28 Å2
Refinement stepCycle: final / Resolution: 2.1→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9179 0 34 210 9423
Biso mean--45.45 41.28 -
Num. residues----1227
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3272X-RAY DIFFRACTION8.888TORSIONAL
12B3272X-RAY DIFFRACTION8.888TORSIONAL
13C3272X-RAY DIFFRACTION8.888TORSIONAL
14D3272X-RAY DIFFRACTION8.888TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.3804840.36872182226658
2.16-2.220.37211280.3553130325884
2.22-2.280.34861330.32793310344389
2.28-2.350.39631430.32173563370696
2.35-2.440.44491450.32893611375697
2.44-2.540.34351510.283837213872100
2.54-2.650.33331510.269637293880100
2.65-2.790.34271500.25237173867100
2.79-2.970.3021490.247136973846100
2.97-3.190.29891520.228537613913100
3.19-3.520.29161520.211737353887100
3.52-4.020.34661400.24343476361693
4.02-5.060.26241450.1933617376296
5.07-33.370.21121530.16583776392999

+
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