[English] 日本語
Yorodumi
- PDB-1djp: CRYSTAL STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1djp
TitleCRYSTAL STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH THE INHIBITOR DON COVALENTLY BOUND IN THE ACTIVE SITE
ComponentsGLUTAMINASE-ASPARAGINASE
KeywordsHYDROLASE / PGA / Glutaminase / Asparaginase / DON / 6-diazo-5-oxo-L-norvaline / Glutaminase-Asparaginase / suicide inhibitor / covalently bound inhibitor
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase activity / periplasmic space
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5,5-dihydroxy-6-oxo-L-norleucine / Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsOrtlund, E. / Lacount, M.W. / Lewinski, K. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2000
Title: Reactions of Pseudomonas 7A glutaminase-asparaginase with diazo analogues of glutamine and asparagine result in unexpected covalent inhibitions and suggests an unusual catalytic triad Thr-Tyr-Glu.
Authors: Ortlund, E. / Lacount, M.W. / Lewinski, K. / Lebioda, L.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1464
Polymers70,7922
Non-polymers3542
Water3,801211
1
A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules

A: GLUTAMINASE-ASPARAGINASE
B: GLUTAMINASE-ASPARAGINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2938
Polymers141,5844
Non-polymers7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area18340 Å2
ΔGint-76 kcal/mol
Surface area36890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.510, 135.910, 137.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein GLUTAMINASE-ASPARAGINASE


Mass: 35396.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. (bacteria) / Strain: 7A / References: UniProt: P10182, glutamin-(asparagin-)ase
#2: Chemical ChemComp-DO2 / 5,5-dihydroxy-6-oxo-L-norleucine


Type: L-peptide linking / Mass: 177.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsUPON REACTION OF 6-DIAZO-5-OXO-L-NORVALINE, A DIAZO ANALOGUE OF GLUTAMINE, THE HET GROUP WAS ...UPON REACTION OF 6-DIAZO-5-OXO-L-NORVALINE, A DIAZO ANALOGUE OF GLUTAMINE, THE HET GROUP WAS TRANSFORMED INTO THE COVALENTLY BOUND INHIBITOR, DO2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0 M Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: ammonium sulfate

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. all: 58567 / Num. obs: 50192 / % possible obs: 85.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 37.8
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.372 / % possible all: 83.7
Reflection shell
*PLUS
% possible obs: 83.7 %

-
Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→48.35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 292804.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4726 10.1 %RANDOM
Rwork0.189 ---
all0.2 48568 --
obs0.189 46995 80.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.39 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2--9.36 Å20 Å2
3----6.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 20 211 5201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.12
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 7340 10.1 %
Rwork0.281 6563 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.PARAM
X-RAY DIFFRACTION3DON.PARDON.TOP
X-RAY DIFFRACTION4DON_AS2.PARDON_AS2.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12

+
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