[English] 日本語
Yorodumi
- PDB-4ee7: Crystal Structure of the Novel Phenazine Prenyltransferase EpzP i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ee7
TitleCrystal Structure of the Novel Phenazine Prenyltransferase EpzP in complex with S-thiolodiphosphate (methylated)
ComponentsPrenyltransferase
KeywordsTRANSFERASE / PT fold / dihydrophenazine carboxylate prenyltransferase
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / TRIHYDROGEN THIODIPHOSPHATE / Prenyltransferase
Function and homology information
Biological speciesStreptomyces cinnamonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.67 Å
AuthorsZocher, G. / Stehle, T.
CitationJournal: Plos One / Year: 2012
Title: Structure-based engineering increased the catalytic turnover rate of a novel phenazine prenyltransferase.
Authors: Zocher, G. / Saleh, O. / Heim, J.B. / Herbst, D.A. / Heide, L. / Stehle, T.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prenyltransferase
B: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,68014
Polymers67,0982
Non-polymers1,58212
Water11,422634
1
A: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3587
Polymers33,5491
Non-polymers8096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3227
Polymers33,5491
Non-polymers7736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.110, 97.010, 135.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Prenyltransferase


Mass: 33549.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: epzP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: E5KWG9

-
Non-polymers , 5 types, 646 molecules

#2: Chemical ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O6P2S
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM (NH4)2SO4, 30% (w/v) PEG2000MME, 100 mM sodium acetate 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2010
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. all: 65578 / Num. obs: 65469 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.67→1.71 Å / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: PHASER / Resolution: 1.67→29.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.287 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22383 2619 4 %RANDOM
Rwork0.18765 ---
obs0.18908 62847 100 %-
all-62847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.67→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 83 634 5197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224718
X-RAY DIFFRACTIONr_bond_other_d0.0010.023166
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9916431
X-RAY DIFFRACTIONr_angle_other_deg0.87237748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52523.895190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5111522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02945
X-RAY DIFFRACTIONr_mcbond_it1.52342911
X-RAY DIFFRACTIONr_mcbond_other0.65841175
X-RAY DIFFRACTIONr_mcangle_it2.1884.54718
X-RAY DIFFRACTIONr_scbond_it2.58151807
X-RAY DIFFRACTIONr_scangle_it3.6175.51702
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 189 -
Rwork0.241 4527 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5978-0.13790.50170.6022-0.04680.6146-0.0053-0.02010.1053-0.0077-0.01-0.0146-0.0541-0.01440.01530.0372-0.01930.01550.0141-0.00990.0137-2.487-17.522215.1308
21.5497-0.05580.45220.7271-0.12430.726-0.08380.02530.1240.03210.0168-0.0001-0.10360.02530.0670.01720.0028-0.00710.02680.01720.01945.1736-17.44252.9943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 292
2X-RAY DIFFRACTION2B5 - 292

+
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