[English] 日本語
Yorodumi
- PDB-3pga: STRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pga
TitleSTRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE
ComponentsGLUTAMINASE-ASPARAGINASE
KeywordsBACTERIAL AMIDOHYDROLASE
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase activity / periplasmic space / cytosol
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
Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas sp. 7A (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLubkowski, J. / Wlodawer, A. / Ammon, H.L. / Copeland, T.D. / Swain, A.L.
Citation
Journal: Biochemistry / Year: 1994
Title: Structural characterization of Pseudomonas 7A glutaminase-asparaginase.
Authors: Lubkowski, J. / Wlodawer, A. / Ammon, H.L. / Copeland, T.D. / Swain, A.L.
#1: Journal: To be Published
Title: Refined Crystal Structure of Acinetobacter Glutaminasificans Glutaminase-Asparaginase
Authors: Lubkowski, J. / Wlodawer, A. / Housset, D. / Weber, I.T. / Ammon, H.L. / Murphy, K.C. / Swain, A.L.
#2: Journal: FEBS Lett. / Year: 1993
Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis: Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of E. Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Molecular Symmetry of Glutaminase-Asparaginases: Rotation Function Studies of the Pseudomonas 7A and Acinetobacter Enzymes
Authors: Ammon, H.L. / Murphy, K.C. / Sjolin, L. / Wlodawer, A. / Holcenberg, J.S. / Roberts, J.
#5: Journal: Biochemistry / Year: 1978
Title: Amino Acid Sequence of the Diazooxonorleucine Binding Site of Acinetobacter and Pseudomonas 7A Glutaminase-Asparaginase Enzymes
Authors: Holcenberg, J.S. / Ericsson, L. / Roberts, J.
#6: Journal: J.Mol.Biol. / Year: 1977
Title: Characterization of Crystals of L-Glutaminase-Asparaginase from Acinetobacter Glutaminasificans and Pseudomonas 7A
Authors: Wlodawer, A. / Roberts, J. / Holcenberg, J.S.
History
DepositionJul 19, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: GLUTAMINASE-ASPARAGINASE
2: GLUTAMINASE-ASPARAGINASE
3: GLUTAMINASE-ASPARAGINASE
4: GLUTAMINASE-ASPARAGINASE


Theoretical massNumber of molelcules
Total (without water)143,9154
Polymers143,9154
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17470 Å2
ΔGint-90 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.260, 130.750, 85.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: GLY 1 19 - THR 1 20C OMEGA = 140.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

-
Components

#1: Protein
GLUTAMINASE-ASPARAGINASE


Mass: 35978.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 7A (bacteria) / References: UniProt: P10182, asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE SEQUENCE OF LUBKOWSKI ET AL., 1994, ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE SEQUENCE OF LUBKOWSKI ET AL., 1994, LISTED IN THE JRNL ARTICLE ABOVE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-35 mg/mlprotein1drop
210 mMphosphate1drop
330-33 %(v/v)MPD1drop
435-38 %(v/v)MPD1reservoir

-
Data collection

ReflectionNum. obs: 81878 / % possible obs: 86 % / Observed criterion σ(I): 1.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Num. measured all: 212153 / Rmerge(I) obs: 0.073

-
Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2.5
Details: IN THIS PDB COORDINATE ENTRY, RESIDUES 1 - 7 IN ALL FOUR CHAINS ARE OMITTED DUE TO DISORDER. FOR RESIDUES 20 - 39, TWO ALTERNATE CONFORMATIONS ARE INCLUDED. (CLOSED CONFORMATION = ALTERNATE ...Details: IN THIS PDB COORDINATE ENTRY, RESIDUES 1 - 7 IN ALL FOUR CHAINS ARE OMITTED DUE TO DISORDER. FOR RESIDUES 20 - 39, TWO ALTERNATE CONFORMATIONS ARE INCLUDED. (CLOSED CONFORMATION = ALTERNATE CONFORMATION CODE C; OPEN CONFORMATION = ALTERNATE CONFORMATION CODE O). THE X, Y, Z COORDINATES AND B FACTORS FOR RESIDUES 20 - 39 OF CHAIN 2 IN THE OPEN CONFORMATION WERE REFINED AGAINST X-RAY DATA. THE COORDINATES FOR THE CLOSED CONFORMATION OF RESIDUES 20 - 39 OF CHAIN 2 AND BOTH CONFORMATIONS OF RESIDUES 20 - 39 IN CHAINS 1, 3, AND 4 WERE NOT REFINED BUT RATHER MODELLED; THE ATOMS OF THESE RESIDUES HAVE AN OCCUPANCY OF 0.0 AND B FACTOR OF 20.0. NOTE THAT RESIDUE 28 WAS TREATED AS GLY (RATHER THAN ALA) IN THE CLOSED CONFORMATION IN THE COORDINATES THAT WERE DEPOSITED. IT HAS BEEN IDENTIFIED AS ALA IN THIS ENTRY. BECAUSE OF THIS THERE ARE NO COORDINATES FOR ATOM CB OF ALA 28 IN THE CLOSED CONFORMATION.
RfactorNum. reflection% reflection
Rwork0.165 --
obs0.165 77141 86 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10436 0 0 418 10854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.1141
X-RAY DIFFRACTIONx_mcangle_it1.9612
X-RAY DIFFRACTIONx_scbond_it2.3361.5
X-RAY DIFFRACTIONx_scangle_it3.8253
Software
*PLUS
Name: X-PLOR/PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.74 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.059
X-RAY DIFFRACTIONx_planar_d0.050.062
X-RAY DIFFRACTIONx_plane_restr0.20.015
X-RAY DIFFRACTIONx_chiral_restr0.20.296

+
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://pdbjlvh1.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