[English] 日本語
Yorodumi
- PDB-3w8x: The complex structure of EncM with trifluorotriketide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w8x
TitleThe complex structure of EncM with trifluorotriketide
ComponentsPutative FAD-dependent oxygenase EncM
KeywordsOXIDOREDUCTASE / monooxygenase / flavin binding
Function / homology
Function and homology information


FAD binding / oxidoreductase activity / identical protein binding
Similarity search - Function
: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 ...: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 6,6,6-trifluoro-1-phenylhexane-1,3,5-trione / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTeufel, R. / Miyanaga, A. / Stull, F. / Michaudel, Q. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
CitationJournal: Nature / Year: 2013
Title: Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement.
Authors: Teufel, R. / Miyanaga, A. / Michaudel, Q. / Stull, F. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
History
DepositionMar 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 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
A: Putative FAD-dependent oxygenase EncM
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0077
Polymers100,8272
Non-polymers2,1805
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-30 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.246, 85.175, 79.363
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative FAD-dependent oxygenase EncM


Mass: 50413.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces maritimus (bacteria) / Gene: encM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or ...References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or internal mixed-function oxidases)
#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-FTK / 6,6,6-trifluoro-1-phenylhexane-1,3,5-trione


Mass: 258.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9F3O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2mM DTT, 0.1M HEPES-Na, 0.2M calcium acetate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 83280 / Num. obs: 83197 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.82→1.85 Å / % possible all: 97

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W8W

3w8w


Resolution: 1.82→48.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.763 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19207 4148 5 %RANDOM
Rwork0.15299 ---
all0.15495 79372 --
obs0.15495 79007 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.336 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20.01 Å2
2---0.58 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7014 0 148 651 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197353
X-RAY DIFFRACTIONr_bond_other_d0.0010.026798
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.97610041
X-RAY DIFFRACTIONr_angle_other_deg1.058315564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33422.579318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.566151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3591564
X-RAY DIFFRACTIONr_chiral_restr0.20.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021730
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.822→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 293 -
Rwork0.229 5505 -
obs--94.77 %
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)
10.1037-0.0195-0.07160.08060.0570.16730.0002-0.01950.01160.00770.01440.01380.00770.0331-0.01470.002-0.0003-0.00520.0227-0.00090.05217.640913.812336.5798
20.0906-0.03320.01550.07950.04480.2321-0.00120.00710.0085-0.02310.00350.01460.01770.0497-0.00230.01550.0055-0.00490.01860.00250.038712.7728-0.11487.1348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 462
2X-RAY DIFFRACTION2B2 - 462

+
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