[English] 日本語
Yorodumi
- PDB-2wk1: Structure of the O-methyltransferase NovP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wk1
TitleStructure of the O-methyltransferase NovP
ComponentsNOVP
KeywordsTRANSFERASE / NOVP / O-METHYLTRANSFERASE / NOVOBIOCIN / TYLF SUPERFAMILY
Function / homology
Function and homology information


demethyldecarbamoylnovobiocin O-methyltransferase / novobiocin biosynthetic process / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Macrocin-O-methyltransferase (TylF) / Macrocin-O-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Demethyldecarbamoylnovobiocin O-methyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES CAERULEUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGomez Garcia, I. / Stevenson, C.E.M. / Uson, I. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: The Crystal Structure of the Novobiocin Biosynthetic Enzyme Novp: The First Representative Structure for the Tylf O-Methyltransferase Superfamily.
Authors: Gomez Garcia, I. / Stevenson, C.E.M. / Uson, I. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Preliminary X-Ray Analysis of the O-Methyltransferase Novp from the Novobiocin-Biosynthetic Cluster of Streptomyces Spheroides.
Authors: Stevenson, C.E.M. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure Determination of the O-Methyltransferase Novp Using the 'Free Lunch Algorithm' as Implemented in Shelxe.
Authors: Uson, I. / Stevenson, C.E.M. / Lawson, D.M. / Sheldrick, G.M.
History
DepositionJun 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NOVP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8766
Polymers32,1751
Non-polymers7015
Water4,360242
1
A: NOVP
hetero molecules

A: NOVP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,75212
Polymers64,3502
Non-polymers1,40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3090 Å2
ΔGint-44.2 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.813, 46.038, 61.220
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2154-

HOH

-
Components

#1: Protein NOVP / O-METHYLTRANSFERASE NOVP


Mass: 32175.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DISULPHIDE BRIDGE BETWEEN CYS228 AND CYS231 / Source: (gene. exp.) STREPTOMYCES CAERULEUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9L9F2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 % / Description: NONE
Crystal growpH: 7 / Details: 2 M AMMONIUM SULPHATE, 100 MM HEPES BUFFER PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.4→36.3 Å / Num. obs: 54638 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.2 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VID

1vid


Resolution: 1.4→34.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.321 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA WERE COLLECTED TO A MAXIMUM RESOLUTION OF 1.35 ANGSTROM, BUT WERE NOT VERY COMPLETE IN THE OUTER RESOLUTION SHELL, SO ONLY THE DATA TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA WERE COLLECTED TO A MAXIMUM RESOLUTION OF 1.35 ANGSTROM, BUT WERE NOT VERY COMPLETE IN THE OUTER RESOLUTION SHELL, SO ONLY THE DATA TO 1.4 ANGSTROM RESOLUTION WERE USED FOR THE REFINEMENT. HOWEVER, THE STRUCTURE WAS SOLVED USING ALL AVAILABLE NATIVE DATA INCLUDING THREE OTHER NATIVE DATA SETS COLLECTED AT LOWER RESOLUTIONS. THIS MERGED NATIVE DATA SET HAS ALSO BEEN DEPOSITED. SEE REFERENCE 2 (USON ET AL., 2007) FOR FURTHER DETAILS.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 2795 5.16 %RANDOM
Rwork0.145 ---
obs0.146 54636 98.8 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.223 Å20 Å2-0.005 Å2
2--0.132 Å20 Å2
3----0.358 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 44 242 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211986
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9742698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79323.33399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55115309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0411520
X-RAY DIFFRACTIONr_chiral_restr0.2590.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3940.2477
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2958
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6350.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4970.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3911.51199
X-RAY DIFFRACTIONr_mcbond_other0.5851.5492
X-RAY DIFFRACTIONr_mcangle_it2.30121924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4473787
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0414.5774
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.4933315
X-RAY DIFFRACTIONr_sphericity_free5.5083328
X-RAY DIFFRACTIONr_sphericity_bonded3.44633302
LS refinement shellResolution: 1.4→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 188 -
Rwork0.395 3485 -
obs--90.78 %

+
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