[English] 日本語
Yorodumi
- PDB-3ayj: X-ray crystal structures of L-phenylalanine oxidase (deaminating ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ayj
TitleX-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism
ComponentsPro-enzyme of L-phenylalanine oxidase
KeywordsOXIDOREDUCTASE / L-PHENYLALANINE OXIDASE / AMINO ACID OXIDASE / FLAVOENZYME / L-Phe Binding
Function / homology
Function and homology information


phenylalanine 2-monooxygenase / phenylalanine 2-monooxygenase activity / nucleotide binding
Similarity search - Function
Polyamine Oxidase; Chain A, domain 2 - #60 / Polyamine Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHENYLALANINE / Phenylalanine 2-monooxygenase precursor
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsIda, K. / Suguro, M. / Suzuki, H.
CitationJournal: J.Biochem. / Year: 2011
Title: High resolution X-ray crystal structures of L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism
Authors: Ida, K. / Suguro, M. / Suzuki, H.
History
DepositionMay 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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 / 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_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: Pro-enzyme of L-phenylalanine oxidase
B: Pro-enzyme of L-phenylalanine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,07710
Polymers155,7992
Non-polymers2,2788
Water42,1012337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-9 kcal/mol
Surface area42490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.985, 112.941, 136.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Pro-enzyme of L-phenylalanine oxidase


Mass: 77899.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: P-501 / Gene: propao / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5W9R9, phenylalanine 2-monooxygenase

-
Non-polymers , 5 types, 2345 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2337 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES PH7.5, 1.0M AMMONIUM SULFATE, pH 7.50, VAPOR DIFFUSION, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.8
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.1→29.2 Å / Num. obs: 615937 / % possible obs: 98.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.398 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YR4

2yr4


Resolution: 1.1→29.2 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.592 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.131 30827 5 %RANDOM
Rwork0.111 ---
obs0.112 584957 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 152 2337 12913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02210852
X-RAY DIFFRACTIONr_bond_other_d0.0050.027121
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.96414830
X-RAY DIFFRACTIONr_angle_other_deg1.1413.00117228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27623.248468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.623151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2521572
X-RAY DIFFRACTIONr_chiral_restr0.1340.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022269
X-RAY DIFFRACTIONr_nbd_refined0.2670.22571
X-RAY DIFFRACTIONr_nbd_other0.2250.28341
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25474
X-RAY DIFFRACTIONr_nbtor_other0.0920.25426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.21707
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0370.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.380.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.299
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.641.58582
X-RAY DIFFRACTIONr_mcbond_other0.8481.52770
X-RAY DIFFRACTIONr_mcangle_it3.15210904
X-RAY DIFFRACTIONr_scbond_it4.62834824
X-RAY DIFFRACTIONr_scangle_it5.8544.53926
X-RAY DIFFRACTIONr_rigid_bond_restr2.306322346
X-RAY DIFFRACTIONr_sphericity_free19.06252337
X-RAY DIFFRACTIONr_sphericity_bonded7.176517697
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 2190 -
Rwork0.164 42333 -
obs--96.85 %

+
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