[English] 日本語
Yorodumi
- PDB-6nxd: TYPE I L-ASPARAGINASE FROM ESCHERICHIA COLI IN COMPLEX WITH CITRA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nxd
TitleTYPE I L-ASPARAGINASE FROM ESCHERICHIA COLI IN COMPLEX WITH CITRATE AT PH 4
ComponentsL-asparaginase 1
KeywordsHYDROLASE / hydrolysis of L-asparagine
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
ASPARAGINE / CITRIC ACID / L-asparaginase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
Authors: Yun, M.K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
History
DepositionFeb 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 15, 2020Group: Advisory / Database references / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal / pdbx_database_related / pdbx_database_remark
Item: _citation.id / _citation_author.citation_id / _exptl_crystal.description
Remark 0THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2P2N, DETERMINED BY YUN, M. ...THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2P2N, DETERMINED BY YUN, M.K., NOURSE, A., WHITE, S.W., ROCK, C.O., HEATH, R.J.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-asparaginase 1
B: L-asparaginase 1
C: L-asparaginase 1
D: L-asparaginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,80035
Polymers157,3424
Non-polymers2,45831
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-100 kcal/mol
Surface area42330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.315, 89.757, 93.083
Angle α, β, γ (deg.)90.000, 117.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
L-asparaginase 1 / L-asparaginase I / L-ASNase I / L-asparagine amidohydrolase I


Mass: 39335.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansA, b1767, JW1756 / Plasmid: pET-15b / Cell (production host): mesophilic bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A962, asparaginase

-
Non-polymers , 5 types, 595 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.14 Å3/Da / Density % sol: 42.41 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2P2N.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: citric acid, sodium chloride, pH 4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 1.9→50 Å / Num. obs: 95017 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Net I/σ(I): 17.9
Reflection shellResolution: 1.9→1.97 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.9→45.17 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.663 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 4749 5 %RANDOM
Rwork0.2029 ---
obs0.205 89764 90.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.22 Å2 / Biso mean: 21.296 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0.28 Å2
2---1.15 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.9→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9692 0 146 564 10402
Biso mean--20.64 26.66 -
Num. residues----1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179237
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.64913639
X-RAY DIFFRACTIONr_angle_other_deg1.3271.56721450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51851255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47723.175485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.404151587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1381549
X-RAY DIFFRACTIONr_chiral_restr0.0760.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021918
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 319 -
Rwork0.237 5893 -
all-6212 -
obs--81.3 %

+
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