[English] 日本語
Yorodumi
- PDB-5k9m: Crystal Structure of PriB Binary Complex with Product Diphosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k9m
TitleCrystal Structure of PriB Binary Complex with Product Diphosphate
ComponentsPriB Prenyltransferase
KeywordsTRANSFERASE / Prenyltransferase / diphosphate / indole-PT / ABBA family / PT fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / PYROPHOSPHATE 2- / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. RM-5-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCao, H. / Elshahawi, S. / Benach, J. / Wasserman, S.R. / Morisco, L.L. / Koss, J.W. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA84374 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI52188 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structure and specificity of a permissive bacterial C-prenyltransferase.
Authors: Elshahawi, S.I. / Cao, H. / Shaaban, K.A. / Ponomareva, L.V. / Subramanian, T. / Farman, M.L. / Spielmann, H.P. / Phillips, G.N. / Thorson, J.S. / Singh, S.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Mar 29, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 23, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.7Sep 27, 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: PriB Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6993
Polymers43,4011
Non-polymers2982
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.727, 83.020, 95.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-934-

HOH

21A-1024-

HOH

-
Components

#1: Protein PriB Prenyltransferase


Mass: 43400.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RM-5-8 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE5*PLUS
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM daptomycin and 1 mM Dimethylallyl diphosphate (DMAPP) with ...Details: PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM daptomycin and 1 mM Dimethylallyl diphosphate (DMAPP) with reservoir solution containing 0.1 M Tris pH 8, 28% w/v PEG 4000. The mixed drops of 0.4 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.5→38.224 Å / Num. obs: 101546 / % possible obs: 99.71 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.59
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 1.7 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.7 / % possible all: 99.79

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INJ

5inj


Resolution: 1.5→38.224 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.61
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3052 3.01 %Random Selection
Rwork0.1935 ---
obs0.1945 101416 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.26 Å2 / Biso mean: 27.3616 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.5→38.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 0 29 426 3118
Biso mean--37.6 35.28 -
Num. residues----353
LS refinement shellResolution: 1.5→1.5234 Å
RfactorNum. reflection% reflection
Rfree0.3929 131 -
Rwork0.4106 4234 -
obs-4365 94 %

+
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