[English] 日本語
Yorodumi
- PDB-7cb4: Crystal structures of of BlAsnase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cb4
TitleCrystal structures of of BlAsnase
ComponentsL-asparaginase
KeywordsHYDROLASE / substrate / complex / mutant
Function / homology
Function and homology information


cellular anatomical structure / asparagine metabolic process / asparaginase / asparaginase activity / metal ion 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
FORMIC ACID / L-asparaginase / asparaginase
Similarity search - Component
Biological speciesBacillus paralicheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLu, F. / Ran, T. / Jiao, L. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31871742 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structures of l-asparaginase from Bacillus licheniformis Reveal an Essential Residue for its Substrate Stereoselectivity.
Authors: Ran, T. / Jiao, L. / Wang, W. / Chen, J. / Chi, H. / Lu, Z. / Zhang, C. / Xu, D. / Lu, F.
History
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,43615
Polymers82,8752
Non-polymers56013
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-74 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.080, 92.080, 230.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein L-asparaginase


Mass: 41437.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus paralicheniformis (bacteria) / Gene: B4121_3474 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q8GMZ7, UniProt: A0A6I7U6Y2*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.037→85.52 Å / Num. obs: 64416 / % possible obs: 99.9 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 20.6
Reflection shellResolution: 2.04→2.09 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4657 / CC1/2: 0.87 / Rpim(I) all: 0.188

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C91

7c91


Resolution: 2.04→85.517 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2036 3207 4.987 %
Rwork0.1822 61106 -
all0.183 --
obs-64313 99.91 %
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: 41.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.571 Å2-0 Å2-0 Å2
2--0.571 Å2-0 Å2
3----1.143 Å2
Refinement stepCycle: LAST / Resolution: 2.04→85.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 33 307 5264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135036
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174715
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6466811
X-RAY DIFFRACTIONr_angle_other_deg2.2971.5810915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92322.68250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13315843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1331528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025669
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021035
X-RAY DIFFRACTIONr_nbd_refined0.2020.2996
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.24611
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22549
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.223
X-RAY DIFFRACTIONr_nbd_other0.1930.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.225
X-RAY DIFFRACTIONr_mcbond_it2.8814.3622553
X-RAY DIFFRACTIONr_mcbond_other2.8814.3622554
X-RAY DIFFRACTIONr_mcangle_it3.6496.5113186
X-RAY DIFFRACTIONr_mcangle_other3.6496.5123187
X-RAY DIFFRACTIONr_scbond_it3.8724.6182483
X-RAY DIFFRACTIONr_scbond_other3.8684.6182474
X-RAY DIFFRACTIONr_scangle_it5.2996.7793625
X-RAY DIFFRACTIONr_scangle_other5.2996.783626
X-RAY DIFFRACTIONr_lrange_it5.99451.2775633
X-RAY DIFFRACTIONr_lrange_other5.99551.2745633
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
2.037-2.0890.2962200.26744320.26846550.880.89399.93560.232
2.089-2.1470.2372210.22343350.22445610.9130.92299.89040.194
2.147-2.2090.1962380.19941950.19944390.9410.93999.86480.176
2.209-2.2770.2392180.19740800.19943040.9210.9499.86060.176
2.277-2.3510.2262060.19439870.19642010.9330.94199.80960.176
2.351-2.4340.2322040.19338490.19540610.9270.94699.8030.175
2.434-2.5260.2261840.19337150.19439080.9360.94499.76970.177
2.526-2.6290.1952140.19835830.19837990.9470.94899.94740.184
2.629-2.7450.2221930.20234170.20336120.9380.94399.94460.191
2.745-2.8790.2291520.19333590.19435120.9370.94699.97150.188
2.879-3.0350.2351540.19531490.19733060.9280.94499.90930.198
3.035-3.2190.231610.19329910.19531520.9430.9491000.204
3.219-3.4410.2021640.1828260.18129900.9470.9571000.197
3.441-3.7160.1971370.16226310.16427680.9560.9641000.186
3.716-4.070.1971200.1624590.16225790.9570.9681000.192
4.07-4.5490.1471080.14522280.14523360.9750.9741000.174
4.549-5.250.1851040.1519820.15220860.9670.9721000.185
5.25-6.4240.181880.19617090.19518000.9620.96299.83330.248
6.424-9.0590.188740.17613550.17614300.9630.96799.93010.232
9.059-85.5170.223470.2388240.2388720.9580.95599.88530.374

+
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