[English] 日本語
Yorodumi
- PDB-3k7q: Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k7q
TitleCrystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans
Components6-hydroxy-L-nicotine oxidase
KeywordsOXIDOREDUCTASE / ENANTIOMERIC SUBSTRATES / FLAVOENZYMES / NICOTINE DEGRADATION / OXIDASE
Function / homology
Function and homology information


(S)-6-hydroxynicotine oxidase / (S)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
: / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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 ...: / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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 / Chem-GP7 / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.05 Å
AuthorsBourenkov, G.P. / Kachalova, G.S. / Bartunik, H.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Analysis of Free and Substrate-Bound 6-Hydroxy-l-Nicotine Oxidase from Arthrobacter nicotinovorans.
Authors: Kachalova, G.S. / Bourenkov, G.P. / Mengesdorf, T. / Schenk, S. / Maun, H.R. / Burghammer, M. / Riekel, C. / Decker, K. / Bartunik, H.D.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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
X: 6-hydroxy-L-nicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8524
Polymers47,2141
Non-polymers1,6383
Water6,702372
1
X: 6-hydroxy-L-nicotine oxidase
hetero molecules

X: 6-hydroxy-L-nicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7048
Polymers94,4282
Non-polymers3,2756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1190 Å2
ΔGint-12 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.988, 162.988, 162.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

-
Components

#1: Protein 6-hydroxy-L-nicotine oxidase


Mass: 47214.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter nicotinovorans (bacteria) / Gene: 6-HLNO / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q93NH4, (S)-6-hydroxynicotine oxidase
#2: Chemical ChemComp-HNL / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / 6-hydroxy-L-nicotine


Mass: 178.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GP7 / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate / 1-pentadecanoyl-2-hexadecanoyl-sn-glycero-3-phosphoethanolamine


Mass: 673.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68NO8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 18, 2001 / Details: KB-mirror
RadiationMonochromator: N2 cooled Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 47039 / Num. obs: 47039 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 31.38 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 22
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3282 / Rsym value: 0.71 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB ENTRY 3K7M

3k7m


Resolution: 2.05→12.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.397 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24967 2343 5 %RANDOM
Rwork0.20159 ---
obs0.20398 44208 99.83 %-
all-44283 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 31.389 Å2
Refinement stepCycle: LAST / Resolution: 2.05→12.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 109 372 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0213520
X-RAY DIFFRACTIONr_angle_refined_deg3.0071.9914799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2823.648159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7315532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1921525
X-RAY DIFFRACTIONr_chiral_restr0.2010.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022693
X-RAY DIFFRACTIONr_nbd_refined0.2790.21833
X-RAY DIFFRACTIONr_nbtor_refined0.3510.22451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2366
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.222
X-RAY DIFFRACTIONr_mcbond_it1.8081.52191
X-RAY DIFFRACTIONr_mcangle_it2.7523434
X-RAY DIFFRACTIONr_scbond_it4.29231574
X-RAY DIFFRACTIONr_scangle_it6.4254.51361
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 176 -
Rwork0.209 3150 -
obs-3150 100 %

+
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