[English] 日本語
Yorodumi
- PDB-5lni: XenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lni
TitleXenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / flavin mononucleotide / complex
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-2H-chromen-2-one / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase / :
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.133 Å
AuthorsWerther, T. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2017
Title: Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase
Authors: Werther, T. / Wahlefeld, S. / Salewski, J. / Kuhlmann, U. / Zebger, I. / Hildebrandt, P. / Dobbek, H.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5469
Polymers39,2891
Non-polymers1,2578
Water8,485471
1
A: NADH:flavin oxidoreductase
hetero molecules

A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,09218
Polymers78,5792
Non-polymers2,51416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6570 Å2
ΔGint-117 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.760, 83.410, 156.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-811-

HOH

21A-846-

HOH

31A-863-

HOH

41A-965-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NADH:flavin oxidoreductase / xenobiotic reductase A


Mass: 39289.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: O999_23785 / Production host: Escherichia coli (E. coli) / References: UniProt: U2SJJ2, UniProt: A0A1X0ZT96*PLUS

-
Non-polymers , 5 types, 479 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 48.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.4 M ammonium sulfate, 0.1 M HEPES/NaOH pH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.13→35 Å / Num. obs: 135813 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.64
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.13-1.160.4233.08190.4
1.16-1.190.3543.71195.2
1.19-1.230.3094.18195.9
1.23-1.270.2754.64196.2
1.27-1.310.235.52196.6
1.31-1.350.1996.34196.9
1.35-1.410.1667.39197
1.41-1.460.1319.02197.3
1.46-1.530.10710.62197.8
1.53-1.60.08812.83197.7
1.6-1.690.07115.22198
1.69-1.790.06117.4198
1.79-1.920.05119.96198.2
1.92-2.070.04323.28198.4
2.07-2.270.04626.87197.8
2.27-2.530.07530.62199.2
2.53-2.930.0633.77199.5
2.93-3.580.04939.16199.3
3.58-5.070.04344.07199.3
5.070.04243.32198.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L5L

3l5l


Resolution: 1.133→29.372 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 12.82
RfactorNum. reflection% reflection
Rfree0.1405 2000 1.47 %
Rwork0.1182 --
obs0.1185 135806 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.25 Å2 / Biso mean: 13.4 Å2 / Biso min: 2.16 Å2
Refinement stepCycle: final / Resolution: 1.133→29.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 119 471 3367
Biso mean--16.37 25.38 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013257
X-RAY DIFFRACTIONf_angle_d1.3954507
X-RAY DIFFRACTIONf_chiral_restr0.077466
X-RAY DIFFRACTIONf_plane_restr0.009601
X-RAY DIFFRACTIONf_dihedral_angle_d12.591214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1331-1.16140.18151310.16868822895390
1.1614-1.19280.16651400.159317945795
1.1928-1.22790.1981410.13999387952896
1.2279-1.26760.19031390.13499392953196
1.2676-1.31290.15081420.12099453959597
1.3129-1.36540.15511420.11019493963597
1.3654-1.42760.14951430.10169526966997
1.4276-1.50280.12911430.09289608975198
1.5028-1.5970.11911430.08849606974998
1.597-1.72030.1121450.08679672981798
1.7203-1.89340.12151450.09479688983398
1.8934-2.16730.12631460.09989762990898
2.1673-2.73020.1131470.115898761002399
2.7302-29.38180.15711530.141102041035799

+
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