[English] 日本語
Yorodumi
- PDB-5ttk: Crystal Structure of Selenomethionine-incorporated Nicotine Oxido... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ttk
TitleCrystal Structure of Selenomethionine-incorporated Nicotine Oxidoreductase from Pseudomonas putida
ComponentsAmine oxidase
KeywordsOXIDOREDUCTASE / nicotine degradation / flavoenzyme / monoamine oxidase family / PHBH
Function / homology
Function and homology information


nicotine dehydrogenase / nicotine catabolic process / alkaloid metabolic process / periplasmic space / oxidoreductase activity / nucleotide binding
Similarity search - Function
Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Nicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsTararina, M.A. / Janda, K.D. / Allen, K.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA041839 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008541 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida.
Authors: Tararina, M.A. / Janda, K.D. / Allen, K.N.
History
DepositionNov 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amine oxidase
B: Amine oxidase
C: Amine oxidase
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,6808
Polymers216,5374
Non-polymers3,1424
Water4,234235
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9202
Polymers54,1341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9202
Polymers54,1341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9202
Polymers54,1341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9202
Polymers54,1341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.102, 126.134, 168.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Amine oxidase /


Mass: 54134.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria)
Strain: S16 / Gene: PPS_4081
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F8G0P2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Description: three-dimensional yellow crystals of rod-like morphology with final dimensions of 0.1 mm by 0.2 mm by 0.5 mm
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1 M sodium citrate tribasic dihydrate pH 8.3, 15% w/v PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.51→48.551 Å / Num. obs: 69981 / % possible obs: 96 % / Redundancy: 5.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.193 / Net I/σ(I): 13.4
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.88 / % possible all: 88

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10.1_2155: 000phasing
PHENIX1.10.1_2155: 000model building
RefinementMethod to determine structure: SAD / Resolution: 2.51→48.551 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 23.79 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2463 2000 2.94 %
Rwork0.2027 --
obs0.204 67949 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→48.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13470 0 212 235 13917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513988
X-RAY DIFFRACTIONf_angle_d0.95318988
X-RAY DIFFRACTIONf_dihedral_angle_d17.0898072
X-RAY DIFFRACTIONf_chiral_restr0.0562068
X-RAY DIFFRACTIONf_plane_restr0.0052434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5102-2.5730.34491110.27493682X-RAY DIFFRACTION75
2.573-2.64260.30611240.26164070X-RAY DIFFRACTION84
2.6426-2.72030.31291320.26744360X-RAY DIFFRACTION89
2.7203-2.80810.2681410.25824639X-RAY DIFFRACTION94
2.8081-2.90850.33751430.24564721X-RAY DIFFRACTION97
2.9085-3.02490.27611470.24064838X-RAY DIFFRACTION98
3.0249-3.16250.27011490.22924898X-RAY DIFFRACTION99
3.1625-3.32920.26281490.22134912X-RAY DIFFRACTION99
3.3292-3.53780.26211480.20254905X-RAY DIFFRACTION99
3.5378-3.81080.24891490.19374898X-RAY DIFFRACTION99
3.8108-4.19410.18741490.17534948X-RAY DIFFRACTION99
4.1941-4.80050.20851510.15484939X-RAY DIFFRACTION99
4.8005-6.04640.20721510.16755004X-RAY DIFFRACTION99
6.0464-48.56010.20191560.16825135X-RAY DIFFRACTION98

+
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