[English] 日本語
Yorodumi
- PDB-2vvl: The structure of MAO-N-D3, a variant of monoamine oxidase from As... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vvl
TitleThe structure of MAO-N-D3, a variant of monoamine oxidase from Aspergillus niger.
Components(MONOAMINE OXIDASE N) x 2
KeywordsOXIDOREDUCTASE / MONOAMINE OXIDASE / ASPERGILLUS NIGER / FAD / PEROXISOME / FLAVOPROTEIN / ENANTIOSELECTIVITY / DIRECTED EVOLUTION VARIANT
Function / homology
Function and homology information


monoamine oxidase activity / monoamine oxidase / peroxisome
Similarity search - Function
Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / 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 / Monoamine oxidase N
Similarity search - Component
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAtkin, K.E. / Hart, S. / Turkenburg, J.P. / Brzozowski, A.M. / Grogan, G.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Structure of Monoamine Oxidase from Aspergillus Niger Provides a Molecular Context for Improvements in Activity Obtained by Directed Evolution.
Authors: Atkin, K.E. / Reiss, R. / Koehler, V. / Bailey, K.R. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Brzozowski, A.M. / Grogan, G.J.
History
DepositionJun 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MONOAMINE OXIDASE N
B: MONOAMINE OXIDASE N
C: MONOAMINE OXIDASE N
D: MONOAMINE OXIDASE N
E: MONOAMINE OXIDASE N
F: MONOAMINE OXIDASE N
G: MONOAMINE OXIDASE N
H: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,44723
Polymers444,7288
Non-polymers6,71915
Water14,538807
1
A: MONOAMINE OXIDASE N
E: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8145
Polymers111,1812
Non-polymers1,6333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-21.7 kcal/mol
Surface area38710 Å2
MethodPQS
2
B: MONOAMINE OXIDASE N
C: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8766
Polymers111,1812
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-8 kcal/mol
Surface area38400 Å2
MethodPQS
3
D: MONOAMINE OXIDASE N
H: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8145
Polymers111,1812
Non-polymers1,6333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-11.3 kcal/mol
Surface area39020 Å2
MethodPQS
4
F: MONOAMINE OXIDASE N
G: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9427
Polymers111,1852
Non-polymers1,7575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-14.2 kcal/mol
Surface area38600 Å2
MethodPQS
Unit cell
Length a, b, c (Å)103.287, 187.248, 132.432
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
MONOAMINE OXIDASE N / MONOAMINE OXIDASE / MAO-N


Mass: 55590.461 Da / Num. of mol.: 7 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FLAVIN ADENINE DINUCLEOTIDE COFACTOR / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: P46882, monoamine oxidase
#2: Protein MONOAMINE OXIDASE N / MONOAMINE OXIDASE / MAO-N


Mass: 55594.449 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FLAVIN ADENINE DINUCLEOTIDE COFACTOR / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: P46882, monoamine oxidase
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN A, ASN 336 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN A, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN B, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN B, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN C, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN C, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN D, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN D, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN E, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN E, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN F, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN F, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN G, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN G, ASN 336 TO SER ENGINEERED RESIDUE IN CHAIN H, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN H, ASN 336 TO SER
Sequence detailsSEQUENCE DISCREPANCIES BETWEEN UNIPROT AND STRUCTURE SEQUENCE AT A300V, L304V AND R450G

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 60.2 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 3350, 0.2M AMMONIUM SULPHATE, 0.1M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 184776 / % possible obs: 97.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.2 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SELENOMET STRUCTURE OF MONOAMINE OXIDASE

Resolution: 2.45→132.45 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.169 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 9016 5 %RANDOM
Rwork0.182 ---
obs0.185 170728 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.24 Å2
2--1.83 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.45→132.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30181 0 452 807 31440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02131217
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9442398
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65353822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95922.71441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.105154700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.78515247
X-RAY DIFFRACTIONr_chiral_restr0.110.24481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02124154
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5761.518894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.102230278
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.732312323
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7274.512112
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 638
Rwork0.226 11357

+
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