[English] 日本語
Yorodumi
- PDB-7rt0: 1.80 A resolution structure of MAO from P. nicotinovorans in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rt0
Title1.80 A resolution structure of MAO from P. nicotinovorans in complex with FAD
Components4-methylaminobutanoate oxidase (methylamine-forming)
KeywordsOXIDOREDUCTASE / MAO / FAD binding / amine oxidase / flavin oxidase / N-methyl-GABA / GABA
Function / homology4-methylaminobutanoate oxidase (methylamine-forming) / nicotine catabolic process / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / 4-methylaminobutanoate oxidase (methylamine-forming)
Function and homology information
Biological speciesPaenarthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.8 Å
AuthorsLovell, S. / Bowman, A. / Battaile, K.P. / Deay, D.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: To be determined
Authors: Bowman, A. / Deay, D.O. / Battaile, K.P. / Lovell, S.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-methylaminobutanoate oxidase (methylamine-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4563
Polymers44,4761
Non-polymers9802
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.302, 51.740, 45.739
Angle α, β, γ (deg.)90.000, 92.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

-
Components

#1: Protein 4-methylaminobutanoate oxidase (methylamine-forming) / Gamma-N-methylaminobutyrate oxidase 2


Mass: 44475.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: mao, ORF56 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE
References: UniProt: Q8GAJ0, 4-methylaminobutanoate oxidase (methylamine-forming)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.47 % / Mosaicity: 0.11 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 20% (w/v) PEG 6000, 0.1 M Bicine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.69 Å / Num. obs: 44295 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.6 / Num. measured all: 303398 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.8-1.847.11.0111866426370.7572100
9-45.696.50.0724843850.99521.399

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å45.68 Å
Translation1.9 Å45.68 Å

-
Processing

Software
NameVersionClassification
PHENIXdev_4273refinement
XDSdata reduction
Aimless0.7.7data scaling
CRANK2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.69 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 2182 4.93 %
Rwork0.1689 42094 -
obs0.1701 44276 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.48 Å2 / Biso mean: 23.1997 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 1.8→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 66 286 3131
Biso mean--18.23 29.81 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.840.24981340.23926482782
1.84-1.880.25661280.212525782706
1.88-1.930.22461280.226172745
1.93-1.980.22331220.177126542776
1.98-2.040.20541270.168525912718
2.04-2.110.2091240.176826242748
2.11-2.180.20331650.174626102775
2.18-2.270.19711290.166626192748
2.27-2.370.17671240.155426202744
2.37-2.50.22131270.150526502777
2.5-2.650.19581510.158426012752
2.65-2.860.16831800.172326112791
2.86-3.140.19551120.175226382750
3.14-3.60.18481490.167426442793
3.6-4.530.18681350.142826722807
4.54-45.690.17391470.178727172864

+
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://pdbjlvh1.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