[English] 日本語
Yorodumi
- PDB-5mzc: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mzc
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-(5-chloro-6-ethoxy-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / KMO
Function / homology
Function and homology information


kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic 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
Chem-8EQ / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å
AuthorsRowland, P.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Development of a Series of Kynurenine 3-Monooxygenase Inhibitors Leading to a Clinical Candidate for the Treatment of Acute Pancreatitis.
Authors: Walker, A.L. / Ancellin, N. / Beaufils, B. / Bergeal, M. / Binnie, M. / Bouillot, A. / Clapham, D. / Denis, A. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Liddle, J. / McBride, A. / ...Authors: Walker, A.L. / Ancellin, N. / Beaufils, B. / Bergeal, M. / Binnie, M. / Bouillot, A. / Clapham, D. / Denis, A. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Liddle, J. / McBride, A. / Mirguet, O. / Mowat, C.G. / Rowland, P. / Tiberghien, N. / Trottet, L. / Uings, I. / Webster, S.P. / Zheng, X. / Mole, D.J.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)104,73413
Polymers101,4792
Non-polymers3,25511
Water13,025723
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5107
Polymers50,7401
Non-polymers1,7706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2246
Polymers50,7401
Non-polymers1,4845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.480, 53.310, 135.840
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 50739.520 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 (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase

-
Non-polymers , 5 types, 734 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-8EQ / 3-(5-chloranyl-6-ethoxy-2-oxidanylidene-1,3-benzoxazol-3-yl)propanoic acid


Mass: 285.680 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H12ClNO5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% glycerol, 14.4% PEG 8000, 0.08 M sodium cacodylate pH 6.5, 0.16 M calcium acetate or 20% glycerol, 16% PEG 8000, 0.08M sodium cacodylate pH 6.5, 0.16M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.82→44 Å / Num. obs: 84627 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.5
Reflection shellResolution: 1.82→1.88 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.93 / Num. unique obs: 8158 / CC1/2: 0.466 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.82→43.84 Å / Cor.coef. Fo:Fc: 0.9634 / Cor.coef. Fo:Fc free: 0.9515 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.21 4295 5.08 %RANDOM
Rwork0.1748 ---
obs0.1766 84585 97.49 %-
Displacement parametersBiso mean: 38.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.2972 Å20 Å20.9835 Å2
2---1.0448 Å20 Å2
3---1.342 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: 1 / Resolution: 1.82→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 0 215 723 7917
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017361HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9610029HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2536SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1234HARMONIC5
X-RAY DIFFRACTIONt_it7361HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion932SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8921SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2837 343 5.6 %
Rwork0.2385 5782 -
all0.2411 6125 -
obs--96.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56130.1232-0.04780.70260.01790.542-0.04380.0906-0.0312-0.09730.0309-0.0014-0.0479-0.0270.0129-0.03370.0146-0.0256-0.0739-0.0259-0.07324.9519-37.942850.1511
21.063-0.2124-0.02090.5918-0.03280.4998-0.0969-0.1765-0.04040.13370.09920.0234-0.0118-0.0552-0.0023-0.04880.0376-0.006-0.0610.0323-0.0954-21.814-8.052215.872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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