[English] 日本語
Yorodumi
- PDB-1v51: The functional role of the binuclear metal center in D-aminoacyla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v51
TitleThe functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation
ComponentsD-aminoacylase
KeywordsHYDROLASE / TIM barrel / beta barrel / insertion
Function / homology
Function and homology information


N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase ...D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Dna Ligase; domain 1 / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-aminoacylase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLai, W.L. / Chou, L.Y. / Ting, C.Y. / Tsai, Y.C. / Liaw, S.H.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The functional role of the binuclear metal center in D-aminoacylase: one-metal activation and second-metal attenuation.
Authors: Lai, W.L. / Chou, L.Y. / Ting, C.Y. / Kirby, R. / Tsai, Y.C. / Wang, A.H. / Liaw, S.H.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism
Authors: Liaw, S.H. / Chen, S.J. / Ko, T.P. / Hsu, C.S. / Chen, C.J. / Wang, A.H. / Tsai, Y.C.
#2: Journal: Protein Sci. / Year: 2002
Title: Structural-based mutational analysis of D-aminoacylase from Alcaligenes faecalis DA1
Authors: Hsu, C.S. / Lai, W.L. / Chang, W.W. / Liaw, S.H. / Tsai, Y.C.
History
DepositionNov 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: D-aminoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,30414
Polymers53,4661
Non-polymers83813
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.134, 77.384, 134.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein D-aminoacylase


Mass: 53466.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: DA1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AGH8, N-acyl-D-amino-acid deacylase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.1 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 199812 / Num. obs: 73910 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.093 / Net I/σ(I): 21.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5 / Num. unique all: 5817 / Rsym value: 0.234 / % possible all: 70.5

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M7J

1m7j


Resolution: 1.6→25.4 Å / Isotropic thermal model: isotropic B / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 7451 -RANDOM
Rwork0.189 ---
all-199812 --
obs-73790 88.2 %-
Displacement parametersBiso mean: 11.68 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 19 255 3863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.202 584 -
Rwork0.188 --
obs-5817 70.5 %

+
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