[English] 日本語
Yorodumi
- PDB-2p2d: Crystal Structure and Allosteric Regulation of the Cytoplasmic Es... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p2d
TitleCrystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli L-Asparaginase I
ComponentsL-ASPARAGINASE I
KeywordsTRANSFERASE / Asparaginase
Function / homology
Function and homology information


asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / protein homotetramerization / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsYun, M.-K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia colil-Asparaginase I
Authors: Yun, M.-K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-ASPARAGINASE I
B: L-ASPARAGINASE I
C: L-ASPARAGINASE I
D: L-ASPARAGINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,44716
Polymers157,3424
Non-polymers1,10512
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-67 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.763, 151.586, 87.142
Angle α, β, γ (deg.)90.00, 88.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-ASPARAGINASE I / E.C.3.5.1.1 / L-asparaginase 1 / L-asparagine amidohydrolase I / L-ASNase I


Mass: 39335.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ansA / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A962, asparaginase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 22.5% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.01259 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01259 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 116888 / Num. obs: 116888 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 7454 / Rsym value: 0.31 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WLS

1wls


Resolution: 1.89→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2183150.92 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5807 5 %RANDOM
Rwork0.184 ---
obs-115353 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2735 Å2 / ksol: 0.368057 e/Å3
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10200 0 72 561 10833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 1.89→1.96 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.229 520 4.8 %
Rwork0.205 10265 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3gol.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

+
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