[English] 日本語
Yorodumi
- PDB-5x6p: Crystal structure of Pseudomonas fluorescens KMO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x6p
TitleCrystal structure of Pseudomonas fluorescens KMO
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase
Function / homology
Function and homology information


kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ metabolic process / NAD+ biosynthetic process / FAD binding
Similarity search - Function
Kynurenine 3-monooxygenase / FAD-binding domain / FAD binding domain / 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 / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKim, H.T. / Hwang, K.Y.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase
Authors: Kim, H.T. / Na, B.K. / Chung, J. / Kim, S. / Kwon, S.K. / Cha, H. / Son, J. / Cho, J.M. / Hwang, K.Y.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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: Kynurenine 3-monooxygenase
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3384
Polymers101,7672
Non-polymers1,5712
Water11,692649
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6692
Polymers50,8841
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area20260 Å2
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6692
Polymers50,8841
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.667, 52.371, 136.271
Angle α, β, γ (deg.)90.00, 103.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Kynurenine 3-monooxygenase / PfKMO / Kynurenine 3-hydroxylase


Mass: 50883.648 Da / Num. of mol.: 2 / Mutation: C252S,C461S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q84HF5, kynurenine 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08 M sodium cacodylate (pH 6.5), 0.16 M calcium acetate, 14.4% polyethylene glycol 8000, and 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→33.75 Å / Num. obs: 91681 / % possible obs: 99.63 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Rsym value: 0.051 / Net I/σ(I): 26.17
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 4573 / CC1/2: 0.957 / Rpim(I) all: 0.279 / Rrim(I) all: 0.498 / Rsym value: 0.41 / Χ2: 0.517 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FN0

5fn0


Resolution: 1.78→33.75 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 21.74
RfactorNum. reflection% reflection
Rfree0.213 4589 5.01 %
Rwork0.1795 --
obs0.1812 91681 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 106 649 7684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077214
X-RAY DIFFRACTIONf_angle_d1.1159818
X-RAY DIFFRACTIONf_dihedral_angle_d13.2532708
X-RAY DIFFRACTIONf_chiral_restr0.0441087
X-RAY DIFFRACTIONf_plane_restr0.0051373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7797-1.79990.25791490.22962793X-RAY DIFFRACTION97
1.7999-1.82110.2261510.222887X-RAY DIFFRACTION100
1.8211-1.84330.23641360.20952896X-RAY DIFFRACTION100
1.8433-1.86660.27011570.22182899X-RAY DIFFRACTION100
1.8666-1.89120.28911530.21862898X-RAY DIFFRACTION100
1.8912-1.91710.26081510.21192836X-RAY DIFFRACTION100
1.9171-1.94450.24181610.19912943X-RAY DIFFRACTION100
1.9445-1.97350.26981590.19042839X-RAY DIFFRACTION100
1.9735-2.00440.2261460.19772901X-RAY DIFFRACTION100
2.0044-2.03720.22571490.19372893X-RAY DIFFRACTION100
2.0372-2.07230.23281290.18592930X-RAY DIFFRACTION100
2.0723-2.110.24181500.18812888X-RAY DIFFRACTION100
2.11-2.15060.21831470.18592861X-RAY DIFFRACTION100
2.1506-2.19450.25751440.18242945X-RAY DIFFRACTION100
2.1945-2.24220.21221660.18682868X-RAY DIFFRACTION100
2.2422-2.29430.23831500.18932936X-RAY DIFFRACTION100
2.2943-2.35170.23551640.18362866X-RAY DIFFRACTION100
2.3517-2.41530.22491570.18732910X-RAY DIFFRACTION100
2.4153-2.48630.24091510.18912894X-RAY DIFFRACTION100
2.4863-2.56650.21571540.19352913X-RAY DIFFRACTION100
2.5665-2.65820.221540.19072896X-RAY DIFFRACTION100
2.6582-2.76460.26011520.1832904X-RAY DIFFRACTION100
2.7646-2.89040.2191220.19012934X-RAY DIFFRACTION100
2.8904-3.04270.21261620.18422910X-RAY DIFFRACTION100
3.0427-3.23320.21281720.1872911X-RAY DIFFRACTION100
3.2332-3.48260.2051690.17542915X-RAY DIFFRACTION100
3.4826-3.83260.18111420.15692906X-RAY DIFFRACTION99
3.8326-4.38610.19511650.15282950X-RAY DIFFRACTION99
4.3861-5.52220.1841450.15712954X-RAY DIFFRACTION99
5.5222-33.75640.1871820.18243016X-RAY DIFFRACTION99

+
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