[English] 日本語
Yorodumi
- PDB-1c0p: D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c0p
TitleD-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES
ComponentsD-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA MOTIF / FLAVIN CONTAINING PROTEIN / OXIDASE
Function / homology
Function and homology information


D-amino acid metabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / FAD binding / peroxisome
Similarity search - Function
D-amino-acid oxidase / D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino-acid oxidase / D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-ALANINE / FLAVIN-ADENINE DINUCLEOTIDE / PEROXIDE ION / D-amino-acid oxidase
Similarity search - Component
Biological speciesRhodosporidium toruloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsUmhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, S.M. / Ghisla, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
Authors: Umhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, M.S. / Ghisla, S.
History
DepositionJul 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6145
Polymers39,6151
Non-polymers9994
Water11,025612
1
A: D-AMINO ACID OXIDASE
hetero molecules

A: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,22710
Polymers79,2302
Non-polymers1,9978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
Unit cell
γ
α
β
Length a, b, c (Å)120.885, 120.885, 136.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-3448-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein D-AMINO ACID OXIDASE /


Mass: 39614.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodosporidium toruloides (fungus) / Plasmid: PT7.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80324, D-amino-acid oxidase

-
Non-polymers , 5 types, 616 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM HEPES 200 MM AMMONIUM SULFATE 16% POLYETHYLENE GLYCOL (PEG) 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMHEPES1drop
2100 mMHEPES1reservoir
315 %PEG100001reservoir
4200 mMammonium sulfate1reservoir
51 mML-lactate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9114
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9114 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 1000770 / Num. obs: 155642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.524 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.2 Å / Num. measured all: 1000779 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7

-
Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementResolution: 1.2→100 Å / σ(F): 4 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.15 7895 -RANDOM AND AS IN RELATED D-AMINO ACID OXIDASE FROM YEAST RHODOTORULA GRACILIS
all0.125 147430 --
obs0.116 125938 5.3 %-
Refinement stepCycle: LAST / Resolution: 1.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 67 612 3466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.57
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 100 Å / σ(F): 4 / Rfactor obs: 0.118 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.116
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.57

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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