[English] 日本語
Yorodumi
- PDB-2dns: The crystal structure of D-amino acid amidase from Ochrobactrum a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dns
TitleThe crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine
ComponentsD-amino acid amidase
KeywordsHYDROLASE / D-stereospecific / Amidase / D-Phenylalanine / penicillin recognize protein
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / D-PHENYLALANINE / D-Amino acid amidase
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOkazaki, S. / Suzuki, A. / Komeda, H. / Asano, Y. / Yamane, T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure and Functional Characterization of a D-Stereospecific Amino Acid Amidase from Ochrobactrum anthropi SV3, a New Member of the Penicillin-recognizing Proteins
Authors: Okazaki, S. / Suzuki, A. / Komeda, H. / Yamaguchi, S. / Asano, Y. / Yamane, T.
History
DepositionApr 26, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 9, 2006ID: 2DD0
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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_atom_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_atom_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-amino acid amidase
B: D-amino acid amidase
C: D-amino acid amidase
D: D-amino acid amidase
E: D-amino acid amidase
F: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,33631
Polymers240,7636
Non-polymers3,57225
Water13,421745
1
A: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9797
Polymers40,1271
Non-polymers8526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5674
Polymers40,1271
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8426
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8426
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5674
Polymers40,1271
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5394
Polymers40,1271
Non-polymers4123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.067, 123.702, 116.046
Angle α, β, γ (deg.)90.00, 104.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBioligical unit of DAA is one molecule. The asymetric unit contain 6 molecules.

-
Components

#1: Protein
D-amino acid amidase


Mass: 40127.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: SV3 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9LCC8
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-DPN / D-PHENYLALANINE


Type: D-peptide linking / Mass: 165.189 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 80647 / Num. obs: 80614 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.11 / Rsym value: 0.099
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 0.434 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
JUPITOR210data reduction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry, 2D83

2d83
PDB Unreleased entry


Resolution: 2.4→19.87 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.88 / SU B: 9.678 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.64 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26873 4106 5 %RANDOM
Rwork0.19548 ---
all0.19917 77883 --
obs0.19917 77883 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16274 0 75 745 17094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02116747
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.95222664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39352071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83123.969771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.349152719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.83315101
X-RAY DIFFRACTIONr_chiral_restr0.0830.22416
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212871
X-RAY DIFFRACTIONr_nbd_refined0.2020.28261
X-RAY DIFFRACTIONr_nbtor_refined0.30.211154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.21042
X-RAY DIFFRACTIONr_metal_ion_refined0.5610.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.220
X-RAY DIFFRACTIONr_mcbond_it0.4721.510363
X-RAY DIFFRACTIONr_mcangle_it0.871216590
X-RAY DIFFRACTIONr_scbond_it1.18636479
X-RAY DIFFRACTIONr_scangle_it1.9064.56073
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 274 -
Rwork0.25 5369 -
obs--94.38 %

+
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