[English] 日本語
Yorodumi
- PDB-6m8u: Crystal structure of UbiX-like FMN prenyltransferase AF1214 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m8u
TitleCrystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, prenylated-FMN complex
ComponentsFlavin prenyltransferase UbiX
KeywordsLYASE / FMN BINDING / UBIX / PRENYL TRANSFERASE
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4LU / PHOSPHATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.221 Å
AuthorsStogios, P.J. / Skarina, T. / Khusnutidinova, A. / Wawrzak, Z. / Yakunin, A.F. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, prenylated-FMN complex
Authors: Stogios, P.J.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin prenyltransferase UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4673
Polymers20,8471
Non-polymers6202
Water2,162120
1
A: Flavin prenyltransferase UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)257,60836
Polymers250,16312
Non-polymers7,44524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area52540 Å2
ΔGint-350 kcal/mol
Surface area62170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.720, 98.720, 98.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-416-

HOH

31A-418-

HOH

-
Components

#1: Protein Flavin prenyltransferase UbiX


Mass: 20846.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: ubiX, AF_1214 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: O29054, flavin prenyltransferase
#2: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O9P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 28% (w/v) PEG400 Cryoprotectant paratone

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 15752 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Net I/σ(I): 38.26
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 799 / CC1/2: 0.937 / Rpim(I) all: 0.332 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EJB

2ejb


Resolution: 2.221→28.498 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 748 5.1 %RANDOM
Rwork0.1573 ---
obs0.1591 14662 95.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.221→28.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 41 120 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171484
X-RAY DIFFRACTIONf_angle_d1.412020
X-RAY DIFFRACTIONf_dihedral_angle_d18.806551
X-RAY DIFFRACTIONf_chiral_restr0.063230
X-RAY DIFFRACTIONf_plane_restr0.023250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2208-2.39220.25171280.19572541X-RAY DIFFRACTION86
2.3922-2.63280.19611450.15932852X-RAY DIFFRACTION97
2.6328-3.01340.20291600.16142820X-RAY DIFFRACTION98
3.0134-3.79510.20011530.15172825X-RAY DIFFRACTION97
3.7951-28.50030.16311620.1472876X-RAY DIFFRACTION99
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)
11.4258-0.32140.26080.3778-0.1120.86650.3462-0.606-0.7410.3651-0.16580.46750.5241-0.35170.30670.3148-0.3339-0.06940.14350.05320.384-18.7137-33.31631.3349
21.7872-1.5197-2.28828.1982-0.7874.01230.39810.4327-1.2786-0.51260.12730.99021.2009-0.209-0.25690.52150.0668-0.24910.2862-0.17310.6801-14.9702-37.8241-12.4177
31.7244-0.1690.07631.6451-0.4440.85580.12720.0321-0.2593-0.0596-0.22340.41690.3246-0.5075-0.06660.1199-0.12850.01310.1954-0.05760.2055-20.3692-23.2206-2.5531
42.34660.363-0.53670.13770.25242.01420.2224-0.0533-0.02480.0007-0.10670.016-0.0204-0.0195-0.11770.0741-0.037-0.01650.04930.00240.1052-3.442-20.1352-0.4898
54.1756-3.65272.23858.3601-0.46331.63740.1018-0.9234-0.89870.93420.1049-0.20690.6855-0.24430.20910.4772-0.1883-0.12670.24380.22980.5831-6.0829-36.672710.3019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:35)
2X-RAY DIFFRACTION2(chain A and resid 36:50)
3X-RAY DIFFRACTION3(chain A and resid 51:121)
4X-RAY DIFFRACTION4(chain A and resid 122:150)
5X-RAY DIFFRACTION5(chain A and resid 151:182)

+
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