[English] 日本語
Yorodumi
- PDB-1hfj: Asparaginase from Erwinia chrysanthemi, hexagonal form with sulfate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hfj
TitleAsparaginase from Erwinia chrysanthemi, hexagonal form with sulfate
ComponentsL-ASPARAGINE AMIDOHYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
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
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPalm, G.J. / Lubkowski, J. / Kozak, M. / Jaskolski, M. / Wlodawer, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups
Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G.J. / Wlodawer, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
#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.
History
DepositionDec 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4384
Polymers70,2462
Non-polymers1922
Water9,278515
1
A: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules

A: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,8768
Polymers140,4924
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area18380 Å2
ΔGint-117.4 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.400, 91.400, 346.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.992362, -0.013099, -0.12266), (-0.01285, -0.97796, 0.208396), (-0.122686, 0.208381, 0.970322)
Vector: -5.99338, 92.47156, -10.14424)
DetailsIN THE TETRAMER TWO ACTIVE SITES ARE FORMED BY EACH INTIMATE DIMER AC AND ITS CRYSTALLOGRAPHIC SYMMETRY MATE

-
Components

#1: Protein L-ASPARAGINE AMIDOHYDROLASE / L-ASPARAGINASE / L-ASNASE


Mass: 35123.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI.
Source: (natural) ERWINIA CHRYSANTHEMI (bacteria) / Strain: NCPPB 1125 / References: UniProt: P06608, asparaginase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 TO 21 IN THE DATABASE ENTRY CONSTITUTE THE LEADER PEPTIDE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.8 / Method: vapor diffusion / Details: Kozak, M., (2000) Acta Biochim. Pol., 47, 807.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mMsodium citrate1drop
346-48 %MPD1reservoir
4100 mMsodium citrate1reservoir
510-20 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: R-AXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1995
RadiationMonochromator: NI FILTER, 0.00025MM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 29191 / % possible obs: 84.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.105 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.55 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.28 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 89335 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 66.8 % / Rmerge(I) obs: 0.28

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
X-PLOR3.1phasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FROM REFERENCE 3

Resolution: 2.4→10 Å / Rfactor Rfree error: 0.0059 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MLF (MAXIMUM LIKELYHOOD ON F'S)
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1371 5 %RANDOM
Rwork0.16 ---
obs0.16 27603 80.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.429 Å2-1.912 Å20 Å2
2---0.429 Å20 Å2
3---0.858 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 10 515 5429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
Refine LS restraints NCSRms dev Biso : 0 Å2 / Rms dev position: 0 Å / Weight Biso : 0 / Weight position: 0
LS refinement shellResolution: 2.4→2.43 Å / Total num. of bins used: 27 /
RfactorNum. reflection
Rfree0.29 -
Rwork0.27 622
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

+
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