[English] 日本語
Yorodumi
- PDB-5xk8: Crystal structure of Isosesquilavandulyl Diphosphate Synthase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xk8
TitleCrystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with GPP
ComponentsUndecaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / antibiotic biosynthesis
Function / homologyditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / polyprenol biosynthetic process / Decaprenyl diphosphate synthase-like superfamily / metal ion binding / GERANYL DIPHOSPHATE / Undecaprenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. CNH189 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsKo, T.P. / Guo, R.T. / Liu, W. / Chen, C.C. / Gao, J.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: "Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase.
Authors: Gao, J. / Ko, T.P. / Chen, L. / Malwal, S.R. / Zhang, J. / Hu, X. / Qu, F. / Liu, W. / Huang, J.W. / Cheng, Y.S. / Chen, C.C. / Yang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T.
History
DepositionMay 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1149
Polymers106,8334
Non-polymers1,2815
Water8,611478
1
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0695
Polymers53,4162
Non-polymers6533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-31 kcal/mol
Surface area17600 Å2
MethodPISA
2
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0454
Polymers53,4162
Non-polymers6282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-17 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.342, 121.151, 121.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Undecaprenyl diphosphate synthase


Mass: 26708.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNH189 (bacteria) / Gene: mcl22 / Plasmid: pET46Ek/LIC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M4T4U9
#2: Chemical
ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5) and 150 mM NaCl RESERVOIR: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 30% PEG 5000MME SOAK: 5 mM MgCl2, 5 mM (NH4)4P2O7, 0.1 M MES pH 6.5, 30% PEG 5000MME, 10 mM GPP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 28, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 42982 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4245 / CC1/2: 0.961 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XK3

5xk3


Resolution: 2.304→24.867 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2122 4.94 %RANDOM
Rwork0.1854 ---
obs0.1869 42934 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→24.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 77 478 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037039
X-RAY DIFFRACTIONf_angle_d0.6119543
X-RAY DIFFRACTIONf_dihedral_angle_d19.1744192
X-RAY DIFFRACTIONf_chiral_restr0.0411038
X-RAY DIFFRACTIONf_plane_restr0.0041233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3042-2.35770.36091310.26342623X-RAY DIFFRACTION98
2.3577-2.41660.28641520.25842710X-RAY DIFFRACTION99
2.4166-2.48190.28861370.24242673X-RAY DIFFRACTION99
2.4819-2.55490.28931230.22842686X-RAY DIFFRACTION99
2.5549-2.63730.28211460.22622679X-RAY DIFFRACTION99
2.6373-2.73140.27261390.22442706X-RAY DIFFRACTION99
2.7314-2.84060.26571420.21732698X-RAY DIFFRACTION99
2.8406-2.96970.25391660.22482700X-RAY DIFFRACTION100
2.9697-3.1260.23391300.21632745X-RAY DIFFRACTION100
3.126-3.32140.22791340.2022698X-RAY DIFFRACTION100
3.3214-3.57720.21831230.17972775X-RAY DIFFRACTION100
3.5772-3.93590.18591290.16032768X-RAY DIFFRACTION100
3.9359-4.50250.17411910.15722722X-RAY DIFFRACTION100
4.5025-5.66160.17771320.13922787X-RAY DIFFRACTION99
5.6616-24.8680.17711470.16782842X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 9.3458 Å / Origin y: 11.7008 Å / Origin z: -10.47 Å
111213212223313233
T0.233 Å2-0.0187 Å20.0041 Å2-0.2392 Å2-0.0227 Å2--0.2664 Å2
L0.164 °2-0.243 °20.3372 °2-0.4749 °2-0.3022 °2--0.8575 °2
S-0.0308 Å °-0.0478 Å °0.0084 Å °-0.0231 Å °-0.022 Å °0.0126 Å °-0.0498 Å °0.0068 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

+
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