[English] 日本語
Yorodumi
- PDB-1ddo: REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ddo
TitleREDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP
ComponentsD-AMINO ACID OXIDASE
KeywordsFLAVOENZYME / FAD COFACTOR / OXIDOREDUCTASE
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / cell projection / peroxisome / extracellular region / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / 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, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / 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-TRYPTOPHAN / FLAVIN-ADENINE DINUCLEOTIDE / IMINO-TRYPTOPHAN / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DENSITY AVERAGING / Resolution: 3.1 Å
AuthorsTodone, F. / Mattevi, A.
CitationJournal: Biochemistry / Year: 1997
Title: Active site plasticity in D-amino acid oxidase: a crystallographic analysis.
Authors: Todone, F. / Vanoni, M.A. / Mozzarelli, A. / Bolognesi, M. / Coda, A. / Curti, B. / Mattevi, A.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-AMINO ACID OXIDASE
B: D-AMINO ACID OXIDASE
C: D-AMINO ACID OXIDASE
D: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,33326
Polymers315,0228
Non-polymers8,31118
Water1,928107
1
A: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9357
Polymers78,7562
Non-polymers2,1805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-35 kcal/mol
Surface area26580 Å2
MethodPISA
2
B: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9357
Polymers78,7562
Non-polymers2,1805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-35 kcal/mol
Surface area26410 Å2
MethodPISA
3
C: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7316
Polymers78,7562
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-35 kcal/mol
Surface area26380 Å2
MethodPISA
4
D: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7316
Polymers78,7562
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-35 kcal/mol
Surface area26470 Å2
MethodPISA
5
C: D-AMINO ACID OXIDASE
D: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,46212
Polymers157,5114
Non-polymers3,9518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-88 kcal/mol
Surface area50110 Å2
MethodPISA
6
A: D-AMINO ACID OXIDASE
B: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,87114
Polymers157,5114
Non-polymers4,35910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-87 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)325.200, 137.100, 196.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.498937, 0.279368, 0.820375), (0.285444, -0.946772, 0.148808), (0.818281, 0.159926, -0.552123)-11.08144, 21.49235, 13.1464
2given(-0.963292, -0.268456, 0.00031), (-0.26668, 0.956783, -0.115968), (0.030835, -0.111794, -0.993253)162.1611, 28.66857, 105.47461
3given(-0.146425, 0.639987, -0.754306), (-0.055335, 0.756032, 0.652192), (0.987673, 0.137236, -0.075288)178.08078, -0.52553, -53.61571
4given(0.735846, -0.616847, -0.279338), (-0.502688, -0.774007, 0.384991), (-0.453691, -0.142874, -0.879632)117.30955, 89.02817, 110.70526
5given(-0.591486, 0.042068, -0.805217), (-0.027869, -0.999108, -0.031727), (-0.805834, 0.003675, 0.59213)167.03641, 56.1406, 85.6049
6given(-0.541988, -0.729343, 0.417502), (0.686024, -0.670926, -0.281479), (0.485407, 0.133858, 0.86398)183.64554, 27.5622, -63.09723
7given(-0.030669, 0.735246, 0.677106), (-0.142578, 0.667279, -0.731034), (-0.989308, -0.118961, 0.084365)91.93096, 81.46582, 101.65317

-
Components

#1: Protein
D-AMINO ACID OXIDASE / DAAO


Mass: 39377.812 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Organelle: PEROXISOME / References: UniProt: P00371, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ITR / IMINO-TRYPTOPHAN


Mass: 202.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H10N2O2
#4: Chemical ChemComp-DTR / D-TRYPTOPHAN


Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.48 Å3/Da / Density % sol: 60 %
Crystal growpH: 8.3
Details: PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 0.6 M / Common name: ammonium succinate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 77977 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 4 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 514100
Reflection shell
*PLUS
% possible obs: 98.7 %

-
Processing

Software
NameVersionClassification
DMmodel building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: DENSITY AVERAGING
Starting model: PDB ENTRY 1KIF

1kif


Resolution: 3.1→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rfree0.25 1000 1.2 %
Rwork0.236 --
all0.236 77977 -
obs0.236 77977 99 %
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21760 0 574 107 22441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.023
X-RAY DIFFRACTIONt_angle_deg3.029
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it6.173
X-RAY DIFFRACTIONt_nbd0.118
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.016

+
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