[English] 日本語
Yorodumi
- PDB-6pvi: Crystal structure of PhqK in complex with paraherquamide L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pvi
TitleCrystal structure of PhqK in complex with paraherquamide L
ComponentsFAD monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / monooxygenase / flavin
Function / homology
Function and homology information


Oxidoreductases / FAD binding / monooxygenase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-OZ7 / FAD-dependent monooxygenase phqK
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsFraley, A.E. / Smith, J.L. / Sherman, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 CA70375 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway.
Authors: Fraley, A.E. / Caddell Haatveit, K. / Ye, Y. / Kelly, S.P. / Newmister, S.A. / Yu, F. / Williams, R.M. / Smith, J.L. / Houk, K.N. / Sherman, D.H.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 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: FAD monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5783
Polymers51,3451
Non-polymers1,2332
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.903, 79.910, 87.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein FAD monooxygenase


Mass: 51345.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium fellutanum (fungus) / Gene: phqK / Plasmid: pKLD116 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L0E4H0
#2: Chemical ChemComp-OZ7 / (8aS,13S,13aR,14aS)-4,4,13,15,15-pentamethyl-12,13,14,14a,15,16-hexahydro-4H,8H,9H,11H-8a,13a-(epiminomethano)[1,4]dioxepino[2,3-a]indolizino[6,7-h]carbazol-17-one


Mass: 447.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 200 mM ammonium acetate, 100 mM Bis-Tris pH 5.5, 2% 2,2,2-trifluoroethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.09→43.843 Å / Num. obs: 345452 / % possible obs: 100 % / Redundancy: 12.6 % / Net I/σ(I): 1.66
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 2646

-
Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.093→43.843 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.47
RfactorNum. reflection% reflection
Rfree0.2563 2574 4.97 %
Rwork0.2079 --
obs0.2103 27473 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.24 Å2 / Biso mean: 57.1915 Å2 / Biso min: 22.08 Å2
Refinement stepCycle: final / Resolution: 2.093→43.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 86 156 3696
Biso mean--57.66 53.86 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.093-2.13280.36021320.3367253395
2.1328-2.17630.32061510.31412792100
2.1763-2.22370.42441440.34112747100
2.2237-2.27540.37271460.31492740100
2.2754-2.33230.40291410.36762754100
2.3323-2.39530.41181430.33822721100
2.3953-2.46580.37671410.33022722100
2.4658-2.54540.37461420.30542746100
2.5454-2.63640.36631420.28062758100
2.6364-2.74190.32731420.27132756100
2.7419-2.86670.28361430.23072748100
2.8667-3.01780.30631400.22132733100
3.0178-3.20680.30481500.20832757100
3.2068-3.45430.25351410.17672740100
3.4543-3.80170.22711460.15972751100
3.8017-4.35140.19041380.14952741100
4.3514-5.48070.17221440.14662731100
5.4807-43.8430.17851480.17052736100
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)
12.08231.1421.02362.02051.17472.58430.04870.09620.0116-0.0251-0.0603-0.03890.03-0.068-0.01320.22150.01270.02420.25390.01750.2842-16.2865-19.699819.2644
24.88721.0872.60391.15840.89112.53850.11160.2565-0.0140.0681-0.0363-0.18730.06120.4501-0.06290.3739-0.02370.01610.36110.00110.35060.0879-8.343327.5644
34.7342-0.50480.76745.30970.63675.5333-0.0577-0.05880.52680.0039-0.0736-0.2035-0.21140.04990.09910.20950.03090.01270.26780.0160.3046-25.3515-11.41117.4572
46.47485.00941.54854.44160.47442.35480.1086-0.61521.12440.3939-0.2328-0.3181-0.58020.31780.09340.58260.01770.01280.6539-0.12170.8864-14.57972.04532.5064
57.51022.32474.55994.35213.89766.4537-0.367-0.37541.0809-0.777-0.27760.5705-0.8035-0.59380.60360.38470.08590.00230.4033-0.05090.5156-35.8401-5.740619.9159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 187 )A7 - 187
2X-RAY DIFFRACTION2chain 'A' and (resid 188 through 309 )A188 - 309
3X-RAY DIFFRACTION3chain 'A' and (resid 310 through 378 )A310 - 378
4X-RAY DIFFRACTION4chain 'A' and (resid 379 through 408 )A379 - 408
5X-RAY DIFFRACTION5chain 'A' and (resid 409 through 448 )A409 - 448

+
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