[English] 日本語
Yorodumi
- PDB-2gez: Crystal structure of potassium-independent plant asparaginase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gez
TitleCrystal structure of potassium-independent plant asparaginase
Components
  • L-asparaginase alpha subunit
  • L-asparaginase beta subunit
KeywordsHYDROLASE / isoaspartyl aminopeptidase / L-asparaginase / Ntn-hydrolase / autoproteolysis / taspase / sodium binding
Function / homology
Function and homology information


beta-aspartyl-peptidase / beta-aspartyl-peptidase activity / proteolysis
Similarity search - Function
(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
Isoaspartyl peptidase/L-asparaginase
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMichalska, K. / Bujacz, G. / Jaskolski, M.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of plant asparaginase.
Authors: Michalska, K. / Bujacz, G. / Jaskolski, M.
#1: Journal: Eur.J.Biochem. / Year: 2004
Title: Expression, purification and catalytic activity of Lupinus luteus asparagine beta-amidohydrolase and its Escherichia coli homolog.
Authors: Borek, D. / Michalska, K. / Brzezinski, K. / Kisiel, A. / Podkowinski, J. / Bonthron, T.D. / Krowarsch, D. / Otlewski, J. / 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: 2000
Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome.
Authors: Borek, D. / Jaskolski, M.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli.
Authors: Prahl, A. / Pazgier, M. / Hejazi, M. / Lockau, W. / Lubkowski, J.
#5: Journal: Nature / Year: 1995
Title: A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.
Authors: Brannigan, J.A. / Dodson, G. / Duggleby, H.J. / Moody, P.C. / Smith, J.L. / Tomchick, D.R. / Murzin, A.G.
#6: Journal: Nat.Struct.Biol. / Year: 1995
Title: Three-dimensional structure of human lysosomal aspartylglucosaminidase.
Authors: Oinonen, C. / Tikkanen, R. / Rouvinen, J. / Peltonen, L.
#7: Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis.
Authors: Guo, H.C. / Xu, Q. / Buckley, D. / Guan, C.
#8: Journal: Structure / Year: 2005
Title: Crystal structure of human Taspase1, a crucial protease regulating the function of MLL.
Authors: Khan, J.A. / Dunn, B.M. / Tong, L.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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
E: L-asparaginase alpha subunit
F: L-asparaginase beta subunit
G: L-asparaginase alpha subunit
H: L-asparaginase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,43818
Polymers139,1338
Non-polymers30510
Water2,018112
1
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)69,7199
Polymers69,5674
Non-polymers1525
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-145 kcal/mol
Surface area21190 Å2
MethodPISA, PQS
2
E: L-asparaginase alpha subunit
F: L-asparaginase beta subunit
G: L-asparaginase alpha subunit
H: L-asparaginase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7199
Polymers69,5674
Non-polymers1525
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-147 kcal/mol
Surface area21040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.68, 60.20, 114.63
Angle α, β, γ (deg.)100.6, 92.9, 113.4
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains two biological assemblies. Each of them is an (alpha/beta)2 heterotetramer or a dimer of (alpha/beta) heterodimers. Subunits alpha (chains A, C, E, G) and beta (chains B, D, F, H) are, respectively, the N- and C-terminal products of autoproteolytic cleavage of a precursor.

-
Components

#1: Protein
L-asparaginase alpha subunit / L-asparagine amidohydrolase


Mass: 21165.877 Da / Num. of mol.: 4 / Fragment: N-terminal subunit (residues 1-192)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Strain: cv. Ventus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIP / References: UniProt: Q9ZSD6, asparaginase
#2: Protein
L-asparaginase beta subunit / L-asparagine amidohydrolase


Mass: 13617.478 Da / Num. of mol.: 4 / Fragment: C-terminal subunit (residues 193-325)
Source method: isolated from a genetically manipulated source
Details: Subunits alpha (chains A, C, E, G) and beta (chains B, D, F, H) are, respectively, the N- and C-terminal products of autoproteolytic cleavage of a precursor
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Strain: cv. Ventus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIP / References: UniProt: Q9ZSD6, asparaginase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 100 mM HEPES, 200 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2004
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 34621 / Num. obs: 34621 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 6.1 / Num. unique all: 3371 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K2X

1k2x


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 22.964 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.349 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1741 5 %RANDOM
Rwork0.189 ---
all0.192 34621 --
obs0.192 32880 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å21.3 Å20.02 Å2
2--4.16 Å20.19 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8693 0 10 112 8815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228823
X-RAY DIFFRACTIONr_bond_other_d0.028244
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.96711962
X-RAY DIFFRACTIONr_angle_other_deg319153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95651171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.663341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1550
X-RAY DIFFRACTIONr_chiral_restr0.0850.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029931
X-RAY DIFFRACTIONr_gen_planes_other0.021635
X-RAY DIFFRACTIONr_nbd_refined0.2250.22014
X-RAY DIFFRACTIONr_nbd_other0.28942
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24340
X-RAY DIFFRACTIONr_nbtor_other0.25154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2283
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.21
X-RAY DIFFRACTIONr_mcbond_it0.4771.55815
X-RAY DIFFRACTIONr_mcbond_other1.52450
X-RAY DIFFRACTIONr_mcangle_it0.87929312
X-RAY DIFFRACTIONr_scbond_it1.47933059
X-RAY DIFFRACTIONr_scangle_it2.5384.52650
LS refinement shellHighest resolution: 2.6 Å / Num. reflection Rwork: 4685 / Total num. of bins used: 10
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)
12.6966-0.4412-0.8651.55550.52981.9216-0.02540.47740.4306-0.26630.0412-0.0507-0.31870.1716-0.0159-0.0068-0.0720.0046-0.05650.05280.00739.750711.1189-10.71
22.0609-0.387-0.16751.71330.44751.8755-0.04920.314-0.18-0.03480.01280.13060.1880.01330.0365-0.0515-0.04120.00220.0512-0.017-0.08795.387-3.4236-13.8382
31.0970.6393-0.15921.8701-0.35911.5110.0236-0.21140.08910.14350.0140.0127-0.02380.0562-0.0376-0.09770.06280.0318-0.102-0.0298-0.0638-10.44291.289314.7101
42.2398-0.0775-0.14221.26450.51721.6128-0.1251-0.0554-0.3559-0.02560.0475-0.12990.25440.12520.0776-0.03990.02340.0253-0.12630.0096-0.0596-4.0657-11.2889.2378
51.378-0.53150.28641.8407-0.16251.42550.01830.1831-0.1371-0.12310.03250.05050.0883-0.0202-0.0508-0.1017-0.0342-0.016-0.1286-0.0293-0.0635-10.551325.624237.4893
62.1706-0.29740.23081.27070.69572.0304-0.1260.07670.3416-0.00670.026-0.0712-0.33090.15740.1-0.0635-0.0311-0.0259-0.14820.0067-0.0406-4.082138.270942.7524
72.45140.73330.66641.6060.18742.41460.0848-0.4256-0.40830.19640.009-0.05150.29560.1487-0.0938-0.03530.06470.0028-0.06850.052-0.00549.806216.133862.9469
82.4531.09930.73471.58980.431.977-0.0303-0.40830.15880.0987-0.02040.1162-0.1782-0.06820.0507-0.03670.0372-0.0031-0.0176-0.0272-0.08635.449730.717165.9204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1595 - 162
2X-RAY DIFFRACTION2BB193 - 3251 - 133
3X-RAY DIFFRACTION3CC2 - 1675 - 170
4X-RAY DIFFRACTION4DD193 - 3251 - 133
5X-RAY DIFFRACTION5EE2 - 1665 - 169
6X-RAY DIFFRACTION6FF193 - 3251 - 133
7X-RAY DIFFRACTION7GG2 - 1595 - 162
8X-RAY DIFFRACTION8HH193 - 3251 - 133

+
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