[English] 日本語
Yorodumi
- PDB-7fhd: Structure of prenyltransferase mutant Y288P from Streptomyces sp.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fhd
TitleStructure of prenyltransferase mutant Y288P from Streptomyces sp. (strain CL190)
ComponentsPrenyltransferase
KeywordsTRANSFERASE / PT-barrel
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / metal ion binding / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsXue, B. / Lim, K.J.H. / Hartono, Y.D. / Go, M.D.K. / Fan, H. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Acs Catalysis / Year: 2022
Title: Structure-Guided Engineering of Prenyltransferase NphB for High-Yield and Regioselective Cannabinoid Production.
Authors: Lim, K.J.H. / Hartono, Y.D. / Xue, B. / Go, M.K. / Fan, H. / Yew, W.S.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prenyltransferase
B: Prenyltransferase
C: Prenyltransferase
D: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)135,4654
Polymers135,4654
Non-polymers00
Water00
1
A: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Prenyltransferase


Theoretical massNumber of molelcules
Total (without water)33,8661
Polymers33,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.2860, 75.1620, 87.6050
Angle α, β, γ (deg.)89.9390, 89.9030, 89.9960
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 41 or resid 46 through 290))
21(chain B and resid 3 through 290)
31(chain C and (resid 3 through 41 or resid 46 through 290))
41(chain D and (resid 3 through 41 or resid 46 through 290))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU(chain A and (resid 3 through 41 or resid 46 through 290))AA3 - 415 - 43
12SERSERHISHIS(chain A and (resid 3 through 41 or resid 46 through 290))AA46 - 29048 - 292
21GLUGLUHISHIS(chain B and resid 3 through 290)BB3 - 2905 - 292
31GLUGLULEULEU(chain C and (resid 3 through 41 or resid 46 through 290))CC3 - 415 - 43
32SERSERHISHIS(chain C and (resid 3 through 41 or resid 46 through 290))CC46 - 29048 - 292
41GLUGLULEULEU(chain D and (resid 3 through 41 or resid 46 through 290))DD3 - 415 - 43
42SERSERHISHIS(chain D and (resid 3 through 41 or resid 46 through 290))DD46 - 29048 - 292

-
Components

#1: Protein
Prenyltransferase


Mass: 33866.305 Da / Num. of mol.: 4 / Mutation: Y288P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria)
Strain: CL190 / Plasmid: pSY5CDF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R2T2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.85 % / Mosaicity: 0.46 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.5→29.2 Å / Num. obs: 13654 / % possible obs: 95.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.211 / Rrim(I) all: 0.339 / Net I/σ(I): 2.2 / Num. measured all: 29344
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.446 / Num. unique obs: 3344 / CC1/2: 0.797 / Rpim(I) all: 0.362 / Rrim(I) all: 0.578 / % possible all: 97.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å29.2 Å
Translation3.2 Å29.2 Å

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZB6

1zb6


Resolution: 3.5→29.2 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.313 764 5.6 %
Rwork0.2426 12881 -
obs0.2466 13645 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.03 Å2 / Biso mean: 29.0734 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 3.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 0 0 8673
Num. residues----1121
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5238X-RAY DIFFRACTION11.761TORSIONAL
12B5238X-RAY DIFFRACTION11.761TORSIONAL
13C5238X-RAY DIFFRACTION11.761TORSIONAL
14D5238X-RAY DIFFRACTION11.761TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.770.29261530.24042645279898
3.77-4.150.36021480.24662617276597
4.15-4.750.2871990.23972475267495
4.75-5.970.29721500.26142544269495
5.97-29.20.34991140.22822600271495

+
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://pdbjlvh1.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