[English] 日本語
Yorodumi
- PDB-4tnu: Human brain aspartoacylase mutant Y231C complex with intermediate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tnu
TitleHuman brain aspartoacylase mutant Y231C complex with intermediate analog (N-phosphonomethyl-L-aspartate)
ComponentsAspartoacylase
KeywordsHYDROLASE / Canavan disease / Zinc-dependent hydrolase / aspartoacylase family / aminoacylase-2 / N-acetyl-L-aspartate
Function / homology
Function and homology information


aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Aspartate and asparagine metabolism / positive regulation of oligodendrocyte differentiation / hydrolase activity, acting on ester bonds / identical protein binding ...aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Aspartate and asparagine metabolism / positive regulation of oligodendrocyte differentiation / hydrolase activity, acting on ester bonds / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #160 / Aspartoacylase / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID / Aspartoacylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E.
CitationJournal: Biochemistry / Year: 2014
Title: Aspartoacylase catalytic deficiency as the cause of canavan disease: a structural perspective.
Authors: Wijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartoacylase
B: Aspartoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0016
Polymers71,4482
Non-polymers5534
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-15 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.959, 147.959, 103.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 10 - 310 / Label seq-ID: 10 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Aspartoacylase / / Aminoacylase-2 / ACY-2


Mass: 35724.051 Da / Num. of mol.: 2 / Mutation: Y231C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPA, ACY2, ASP / Plasmid: pPICZA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P45381, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AS9 / N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID / N-PHOSPHONOMETHYL-L-ASPARTIC ACID / (2S)-2-(HYDROPEROXY(METHOXY)PHOSPHORYLAMINO)SUCCINIC ACID


Type: L-peptide linking / Mass: 211.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG 3350, 0.05M sodium citrate, 0.3M potassium phosphate (dibasic), 3% ethylene glycol, 0.01M DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.283 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25970 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O4H

2o4h


Resolution: 2.9→48.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.541 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.572 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23473 1320 5.1 %RANDOM
Rwork0.19724 ---
obs0.19913 24598 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2--1.59 Å20 Å2
3----3.17 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 28 24 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194974
X-RAY DIFFRACTIONr_bond_other_d0.0030.024760
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.976742
X-RAY DIFFRACTIONr_angle_other_deg0.879311002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7224.483232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50115870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.281524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215560
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021112
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.946.8762412
X-RAY DIFFRACTIONr_mcbond_other3.946.8772413
X-RAY DIFFRACTIONr_mcangle_it6.10610.3093008
X-RAY DIFFRACTIONr_mcangle_other6.10410.313008
X-RAY DIFFRACTIONr_scbond_it3.8177.2032561
X-RAY DIFFRACTIONr_scbond_other3.8167.2032562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.20710.6423735
X-RAY DIFFRACTIONr_long_range_B_refined8.74453.1885381
X-RAY DIFFRACTIONr_long_range_B_other8.74353.1875381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18706 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 103 -
Rwork0.323 1703 -
obs--96.32 %

+
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