[English] 日本語
Yorodumi
- PDB-3c17: Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Pept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c17
TitleHexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation
ComponentsL-asparaginase precursor
KeywordsHYDROLASE / ISOASPARTYL PEPTIDASE / ASPARAGINASE / NTN-HYDROLASE / AUTOPROTEOLYSIS / PRECURSOR
Function / homology
Function and homology information


beta-aspartyl-peptidase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm
Similarity search - Function
Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Isoaspartyl peptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMichalska, K. / Hernandez-Santoyo, A. / Jaskolski, M.
Citation
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.
#1: Journal: To be Published
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / 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: J.Mol.Biol. / Year: 2006
Title: Crystal structure of plant asparaginase
Authors: Michalska, K. / Bujacz, G. / Jaskolski, M.
#5: 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.
#6: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural insights into the mechanism of intramolecular proteolysis
Authors: Xu, Q. / Buckley, D. / Guan, C. / Guo, H.-C.
#7: Journal: J.Biol.Chem. / Year: 1998
Title: Characterization and functional analysis of the cis-autoproteolysis active center of glycosylasparaginase
Authors: Guan, C. / Liu, Y. / Shao, Y. / Cui, T. / Liao, W. / Ewel, A. / Whitaker, R. / Paulus, H.
#8: Journal: J.Biol.Chem. / Year: 1998
Title: Activation and oligomerization of aspartylglucosaminidase
Authors: Saarela, J. / Laine, M. / Tikkanen, R. / Oinonen, C. / Jalanko, A. / Rouvinen, J. / Peltonen, L.
#9: Journal: Structure / Year: 2003
Title: A dual role for an aspartic acid in glycosylasparaginase autoproteolysis
Authors: Qian, X. / Guan, C. / Guo, H.-C.
#10: 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.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-asparaginase precursor
B: L-asparaginase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,38130
Polymers66,5252
Non-polymers85628
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-289.4 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.4700, 149.4700, 214.3500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein L-asparaginase precursor / L-asparagine amidohydrolase


Mass: 33262.676 Da / Num. of mol.: 2 / Mutation: T179A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: THE N-TERMINAL METHIONINE WAS REMOVED BY E. COLI INTRACELLULAR AMINOPEPTIDASE
Gene: ybiK (iaaA) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P37595, beta-aspartyl-peptidase, asparaginase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 5.2 Å3/Da / Density % sol: 76.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4.3M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.67 Å / Num. all: 98405 / Num. obs: 98405 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.2 / Num. unique all: 14515 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K2X

1k2x


Resolution: 1.95→44.51 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.255 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: R-FREE / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. MAXIMUM LIKELIHOOD TARGET. THE REFINEMENT INCLUDED TLS PARAMETERS. THE RESIDUES 160-167 AND 315-321 FROM CHAIN A AS WELL AS 162-167 AND 314-321 ...Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. MAXIMUM LIKELIHOOD TARGET. THE REFINEMENT INCLUDED TLS PARAMETERS. THE RESIDUES 160-167 AND 315-321 FROM CHAIN A AS WELL AS 162-167 AND 314-321 FROM CHAIN B WERE NOT MODELED DUE TO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 992 1 %RANDOM
Rwork0.184 ---
obs0.184 97402 95.75 %-
all-97402 --
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: 27.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0.83 Å20 Å2
2---1.66 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 28 434 4904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224577
X-RAY DIFFRACTIONr_bond_other_d0.0010.023026
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9736204
X-RAY DIFFRACTIONr_angle_other_deg0.94837407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93924.27185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57615754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9491532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
X-RAY DIFFRACTIONr_nbd_refined0.2270.2976
X-RAY DIFFRACTIONr_nbd_other0.1950.23509
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22259
X-RAY DIFFRACTIONr_nbtor_other0.090.22442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2354
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.060.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.21
X-RAY DIFFRACTIONr_mcbond_it0.6311.53035
X-RAY DIFFRACTIONr_mcbond_other0.1741.51288
X-RAY DIFFRACTIONr_mcangle_it1.1124798
X-RAY DIFFRACTIONr_scbond_it1.96731567
X-RAY DIFFRACTIONr_scangle_it3.1624.51397
LS refinement shellResolution: 1.95→2.055 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.249 137 -
Rwork0.255 14351 -
obs-14351 98.11 %
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)
11.86020.4992-0.14042.2684-0.81611.35950.0866-0.00890.23840.2178-0.03690.0445-0.1767-0.0396-0.0497-0.0517-0.0469-0.0207-0.1917-0.0131-0.1908-63.089439.593635.3131
21.29340.3068-0.41872.2092-0.7221.22920.04960.0047-0.13810.1106-0.1248-0.4361-0.05710.24640.0751-0.0755-0.0715-0.0572-0.1230.0187-0.1338-51.499829.523935.7534
31.94920.6343-0.11762.4537-0.69111.0994-0.05220.2247-0.122-0.26980.10810.19060.1486-0.132-0.05590.0001-0.091-0.0728-0.1412-0.0351-0.1519-77.78089.302127.8186
42.07020.71430.01471.7415-0.5321.0760.0064-0.0832-0.26750.0664-0.0295-0.11230.19080.05290.0231-0.0079-0.0466-0.0368-0.1879-0.0035-0.1017-67.2186.349938.3755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1591 - 158
2X-RAY DIFFRACTION2AA168 - 314167 - 313
3X-RAY DIFFRACTION3BB2 - 1611 - 160
4X-RAY DIFFRACTION4BB168 - 313167 - 312

+
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