[English] 日本語
Yorodumi
- PDB-6pgm: PirF geranyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pgm
TitlePirF geranyltransferase
ComponentsPirF Geranyltransferase
KeywordsTRANSFERASE / geranylation / cyanobactin
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / Putative prenyl transferase
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7005 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNair, S.K. / Hao, Y. / Estrada, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2018
Title: A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases.
Authors: Estrada, P. / Morita, M. / Hao, Y. / Schmidt, E.W. / Nair, S.K.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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: PirF Geranyltransferase
B: PirF Geranyltransferase


Theoretical massNumber of molelcules
Total (without water)69,9722
Polymers69,9722
Non-polymers00
Water3,189177
1
A: PirF Geranyltransferase


Theoretical massNumber of molelcules
Total (without water)34,9861
Polymers34,9861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PirF Geranyltransferase


Theoretical massNumber of molelcules
Total (without water)34,9861
Polymers34,9861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.898, 93.911, 93.831
Angle α, β, γ (deg.)90.00, 128.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21B-379-

HOH

-
Components

#1: Protein PirF Geranyltransferase / Putative prenyl transferase


Mass: 34986.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7005 (bacteria)
Gene: pirF / Production host: Escherichia coli (E. coli) / References: UniProt: J3S802, Transferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Bis-tris propane, sodium citrate, ammonium sulfate / PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 14, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→48.1 Å / Num. obs: 37152 / % possible obs: 98.2 % / Redundancy: 5.1 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.32 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
pointlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TTY

5tty


Resolution: 2.3→48.082 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.02
RfactorNum. reflection% reflection
Rfree0.268 1848 4.99 %
Rwork0.2243 --
obs0.2265 37000 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 177 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084984
X-RAY DIFFRACTIONf_angle_d0.966715
X-RAY DIFFRACTIONf_dihedral_angle_d3.2512987
X-RAY DIFFRACTIONf_chiral_restr0.057720
X-RAY DIFFRACTIONf_plane_restr0.006859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36210.33321220.28232655X-RAY DIFFRACTION98
2.3621-2.43160.32851550.27682691X-RAY DIFFRACTION100
2.4316-2.51010.32091280.27162728X-RAY DIFFRACTION100
2.5101-2.59980.31741370.26792705X-RAY DIFFRACTION100
2.5998-2.70390.31861420.26222679X-RAY DIFFRACTION100
2.7039-2.8270.31791680.25662684X-RAY DIFFRACTION100
2.827-2.9760.33551230.26262722X-RAY DIFFRACTION100
2.976-3.16240.31541340.2382705X-RAY DIFFRACTION100
3.1624-3.40650.29441540.23212704X-RAY DIFFRACTION100
3.4065-3.74920.26251500.20152712X-RAY DIFFRACTION100
3.7492-4.29140.23781410.19692725X-RAY DIFFRACTION100
4.2914-5.40560.20231380.18082703X-RAY DIFFRACTION99
5.4056-48.0930.23231560.2222739X-RAY DIFFRACTION99

+
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