[English] 日本語
Yorodumi
- PDB-4pu6: Crystal structure of potassium-dependent plant-type L-asparaginas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pu6
TitleCrystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ cations
Components
  • L-ASPARAGINASE ALPHA SUBUNIT
  • L-ASPARAGINASE BETA SUBUNIT
KeywordsHYDROLASE / metal binding sites / potassium coordination / K-dependent enzyme / Ntn-hydrolase / plant protein / L-asparaginase / isoaspartyl aminopeptidase / amidohydrolase
Function / homology
Function and homology information


(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / : / Isoaspartyl peptidase/L-asparaginase 2
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBejger, M. / Gilski, M. / Imiolczyk, B. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase
Authors: Bejger, M. / Imiolczyk, B. / Clavel, D. / Gilski, M. / Pajak, A. / Marsolais, F. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of plant asparaginase.
Authors: Michalska, K. / Bujacz, G. / Jaskolski, M.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate
Authors: Michalska, K. / Brzezinski, K. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M.
#4: Journal: J.Biol.Chem. / Year: 2008
Title: The mechanism of autocatalytic activation of plant-type L-asparaginases
Authors: Michalska, K. / Hernandez-Santoyo, A. / Jaskolski, M.
#5: Journal: ACTA BIOCHIM.POL. / Year: 2006
Title: Structural aspects of L-asparaginases, their friends and relations
Authors: Michalska, K. / Jaskolski, M.
#6: Journal: Eur.J.Biochem. / Year: 2004
Title: Expression, purification and catalytic activity of Lupinus luteus asparagine -amidohydrolase and its Escherichia coli homolog
Authors: Borek, D. / Michalska, K. / Brzezinski, K. / Kisiel, A. / Podkowinski, J. / Bonthron, D.T. / Krowarsch, D. / Otlewski, J. / Jaskolski, M.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by Escherichia coli genome.
Authors: Borek, D. / Jaskolski, M.
#8: Journal: ACTA BIOCHIM.POL. / Year: 2001
Title: Sequence analysis of enzymes with asparaginase activity
Authors: Borek, D. / Jaskolski, M.
#9: Journal: Biochemistry / Year: 2012
Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis
Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A.
#10: Journal: Chem.Biol. / Year: 2013
Title: Free glicyne accelerates the autoproteolytic activation of human asparaginase
Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / McSorley, T. / Konrad, M. / Lavie, A.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 ALPHA SUBUNIT
B: L-ASPARAGINASE BETA SUBUNIT
C: L-ASPARAGINASE ALPHA SUBUNIT
D: L-ASPARAGINASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5709
Polymers69,2814
Non-polymers2895
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-94 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.938, 102.672, 127.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein L-ASPARAGINASE ALPHA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 21015.805 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SUBUNIT ALPHA (UNP residues 1-195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#2: Protein L-ASPARAGINASE BETA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 13624.618 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SUBUNIT BETA (UNP residues 196-326)
Source method: isolated from a genetically manipulated source
Details: SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR.
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DIFFERENCE (POLYMORPHISM) AT POSITION 17 REFLECTS A DIFFERENT CULTIVAR (AC COMPASS).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 0.1M bis tris propane, 0.2M sodium nitrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI -111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→47.6 Å / Num. obs: 32518 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 57.38 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.97
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.98 / % possible all: 78.8

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEZ

2gez


Resolution: 2.3→47.6 Å / SU ML: 0.27 / Phase error: 27.94 / Stereochemistry target values: ENGH & HUBER / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.231 1009 3.1 %
Rwork0.176 --
obs0.177 32518 96.3 %
all-32518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 13 114 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184313
X-RAY DIFFRACTIONf_angle_d1.4665835
X-RAY DIFFRACTIONf_dihedral_angle_d14.8991565
X-RAY DIFFRACTIONf_chiral_restr0.091673
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.323 111 -
Rwork0.2834 3454 -
obs--76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7284-0.87540.81731.6448-0.06962.34020.13020.45640.0037-1.0089-0.0337-0.0074-0.0807-0.1107-0.09341.0420.0394-0.04790.34910.00290.2240.769228.23849.7554
21.6650.0244-0.5313.8548-0.60373.18450.18010.00930.0513-0.1769-0.0622-0.1631-0.68210.214-0.09240.3511-0.04690.02940.2278-0.04340.19692.719127.132923.4807
30.4646-0.18450.09031.64170.971.19020.0523-0.4570.27590.60340.0160.5622-0.4903-0.1716-0.06010.5912-0.06220.13030.3515-0.03850.1278-2.800821.695435.3971
45.9161-1.6190.7530.5255-0.69933.08120.030.4542-0.3837-0.472-0.07470.17670.1911-0.0227-0.03990.26770.0838-0.28620.8541-0.09831.1422-18.59816.510717.5464
50.3251-0.5201-0.42632.1929-0.50662.20640.555-0.0669-0.218-0.926-0.2547-0.3421-0.45350.2527-0.13470.3574-0.06290.20870.2955-0.00950.22967.077820.224819.0946
63.57431.2717-0.8174.74350.18894.72960.08490.5768-0.2541-0.7433-0.26040.21680.0819-0.05770.0750.71370.0512-0.03330.3157-0.02230.20873.76939.16813.5253
71.76490.1169-2.94173.5593-0.98615.0748-0.07080.0594-0.1736-0.263-0.1106-0.64670.06330.75460.10670.76430.11380.78030.47090.15560.576517.877914.332211.1185
81.8272-0.4711-0.84421.2384-0.16252.68360.04260.3034-0.0787-0.36120.098-0.2501-0.06930.3502-0.03021.6030.15191.07990.51590.1134-0.729214.737416.74883.0707
91.4817-0.1791-0.182.3182-1.40320.8841-0.252-0.2904-0.2570.0925-0.1946-0.9920.35070.87710.27530.37790.17740.04520.59390.26061.010521.7953-8.35430.6371
102.5225-0.6629-0.18823.47630.01362.2659-0.1395-0.3278-0.8789-0.1686-0.1312-0.75290.03240.4690.22810.38730.08620.09170.37620.22150.701212.185-10.839832.4582
112.7230.05620.29854.8715-0.14423.80420.06510.0186-0.4305-0.7768-0.09040.10640.28560.25560.04680.30450.04460.06980.21410.04280.29983.8393-1.257423.7023
120.6746-0.4401-0.14943.0861-0.44061.3220.1489-0.0935-0.5872-0.3339-0.18180.97680.0702-0.2760.05340.2111-0.0645-0.01170.26850.02150.4257-3.6213-0.249525.6722
136.30771.02065.05432.2340.9635.7479-0.093-0.324-0.22140.7811-0.24770.12280.45930.03070.22030.5185-0.02940.14290.32170.16670.4368-0.6942-6.373940.5643
140.8716-0.83370.18632.7913-2.83653.5687-0.1257-0.25470.07660.22820.2241-0.9556-0.3220.49870.06270.99360.0123-0.40890.83940.26030.684615.22863.135449.74
152.07320.2879-0.76453.3707-1.35492.2889-0.1169-0.0526-0.3623-0.3523-0.2492-1.18820.32510.47510.22360.2050.03160.04920.35970.12870.495313.3811.163224.6332
160.0406-0.00210.00331.5206-1.87652.3085-0.04760.2936-0.047-0.51990.0188-0.3378-0.270.3466-0.01870.84060.12550.5410.61170.20710.782120.46985.229412.451
171.1665-0.4392-0.91760.32151.08664.3424-0.06610.19680.0668-0.32310.0488-0.3125-0.25550.5741-0.00630.61310.14110.59830.94240.34651.453228.29721.938815.8565
181.172-0.50040.82311.2557-0.24273.902-0.45440.10210.2078-0.2909-0.0264-0.3071-0.44790.64850.36150.4417-0.04010.22150.66510.18741.055823.83034.136524.0551
190.0972-0.28290.20490.7692-0.62920.5206-0.0155-0.0015-0.2359-0.58-0.2594-0.73360.33510.64310.13840.28330.21610.32070.86420.37041.564125.4054-9.51224.4596
202.9973-1.31720.75450.8043-0.93691.79280.43330.6607-0.6053-0.53190.0821-0.0050.51740.1284-0.35981.04640.10370.16520.4545-0.11880.27616.384215.27898.101
210.3961-0.4855-0.16870.6454-0.02760.76740.20660.49790.2074-0.801-0.1908-0.4452-0.33610.3275-0.06321.56950.0760.36870.5286-0.00190.04818.362828.39897.0689
222.00289.54963.36317.03331.16912.9621-0.19310.5983-0.0773-1.00630.2825-0.43450.03990.36690.04151.36820.1343-0.05950.62320.1189-0.04240.749930.97093.6103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 196 through 247 )
6X-RAY DIFFRACTION6chain 'B' and (resid 248 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 267 )
8X-RAY DIFFRACTION8chain 'B' and (resid 268 through 282 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 19 )
10X-RAY DIFFRACTION10chain 'C' and (resid 20 through 80 )
11X-RAY DIFFRACTION11chain 'C' and (resid 81 through 103 )
12X-RAY DIFFRACTION12chain 'C' and (resid 104 through 132 )
13X-RAY DIFFRACTION13chain 'C' and (resid 133 through 144 )
14X-RAY DIFFRACTION14chain 'C' and (resid 145 through 158 )
15X-RAY DIFFRACTION15chain 'D' and (resid 196 through 256 )
16X-RAY DIFFRACTION16chain 'D' and (resid 257 through 268 )
17X-RAY DIFFRACTION17chain 'D' and (resid 269 through 282 )
18X-RAY DIFFRACTION18chain 'D' and (resid 283 through 295 )
19X-RAY DIFFRACTION19chain 'D' and (resid 296 through 326 )
20X-RAY DIFFRACTION20chain 'B' and (resid 283 through 295 )
21X-RAY DIFFRACTION21chain 'B' and (resid 296 through 319 )
22X-RAY DIFFRACTION22chain 'B' and (resid 320 through 326 )

+
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