[English] 日本語
Yorodumi
- PDB-6fyf: The crystal structure of EncM V135M mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fyf
TitleThe crystal structure of EncM V135M mutant
ComponentsPutative FAD-dependent oxygenase EncM
KeywordsFLAVOPROTEIN / monooxygenase / flavin-N5-oxide / FAD / EncM / oxygenating species / oxygen 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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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 / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaleem-Batcha, R. / Teufel, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTE931/2-1 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Enzymatic control of dioxygen binding and functionalization of the flavin cofactor.
Authors: Saleem-Batcha, R. / Stull, F. / Sanders, J.N. / Moore, B.S. / Palfey, B.A. / Houk, K.N. / Teufel, R.
History
DepositionMar 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: Putative FAD-dependent oxygenase EncM
B: Putative FAD-dependent oxygenase EncM
C: Putative FAD-dependent oxygenase EncM
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,5688
Polymers200,4264
Non-polymers3,1424
Water10,845602
1
A: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8922
Polymers50,1061
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8922
Polymers50,1061
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8922
Polymers50,1061
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8922
Polymers50,1061
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.268, 175.164, 130.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein
Putative FAD-dependent oxygenase EncM


Mass: 50106.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces maritimus (bacteria) / Gene: encM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KHK2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES-Na, 0.2M Calcium Acetate, 20% - 30% PEG 3350, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.2→48.05 Å / Num. obs: 93709 / % possible obs: 99.6 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.51

-
Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XLO

4xlo


Resolution: 2.2→43.959 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 32.2
RfactorNum. reflection% reflection
Rfree0.2741 4784 5.12 %
Rwork0.2253 --
obs0.2279 93459 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13864 0 212 602 14678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814453
X-RAY DIFFRACTIONf_angle_d0.80919732
X-RAY DIFFRACTIONf_dihedral_angle_d18.1125088
X-RAY DIFFRACTIONf_chiral_restr0.0562140
X-RAY DIFFRACTIONf_plane_restr0.0052564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.34181370.27842946X-RAY DIFFRACTION99
2.225-2.25120.33861510.25752918X-RAY DIFFRACTION97
2.2512-2.27860.32381430.25982876X-RAY DIFFRACTION98
2.2786-2.30750.33331780.25792908X-RAY DIFFRACTION99
2.3075-2.33780.3451510.25312954X-RAY DIFFRACTION100
2.3378-2.36990.3171500.2622967X-RAY DIFFRACTION100
2.3699-2.40370.35511610.2562913X-RAY DIFFRACTION100
2.4037-2.43960.36341440.25272970X-RAY DIFFRACTION100
2.4396-2.47770.31671380.25123005X-RAY DIFFRACTION100
2.4777-2.51830.29771490.24892936X-RAY DIFFRACTION100
2.5183-2.56180.34871580.25742947X-RAY DIFFRACTION100
2.5618-2.60830.33791390.2522976X-RAY DIFFRACTION100
2.6083-2.65850.33531690.25342936X-RAY DIFFRACTION100
2.6585-2.71270.28351640.24782934X-RAY DIFFRACTION100
2.7127-2.77170.31681800.25382933X-RAY DIFFRACTION100
2.7717-2.83620.30711720.24742960X-RAY DIFFRACTION100
2.8362-2.90710.29611890.24762911X-RAY DIFFRACTION100
2.9071-2.98570.27461930.24692945X-RAY DIFFRACTION100
2.9857-3.07350.30481810.23632925X-RAY DIFFRACTION100
3.0735-3.17270.29921600.23442933X-RAY DIFFRACTION99
3.1727-3.28610.32381630.2332871X-RAY DIFFRACTION97
3.2861-3.41760.27381490.233013X-RAY DIFFRACTION100
3.4176-3.57310.25741550.22352971X-RAY DIFFRACTION100
3.5731-3.76130.22711630.20342978X-RAY DIFFRACTION100
3.7613-3.99690.2691830.20522962X-RAY DIFFRACTION100
3.9969-4.30520.23361480.19193005X-RAY DIFFRACTION100
4.3052-4.7380.22091440.17843010X-RAY DIFFRACTION100
4.738-5.42250.23541590.18673008X-RAY DIFFRACTION99
5.4225-6.82770.23531580.22082993X-RAY DIFFRACTION98
6.8277-43.96750.18311550.213071X-RAY DIFFRACTION96

+
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