[English] 日本語
Yorodumi
- PDB-3tfl: LytR-Cps2a-Psr family protein with bound octaprenyl pyrophosphate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tfl
TitleLytR-Cps2a-Psr family protein with bound octaprenyl pyrophosphate lipid
ComponentsCPS2A, Integral membrane regulatory protein Wzg
KeywordsTRANSFERASE / bacterial cell wall techoic acid synthesis
Function / homology
Function and homology information


DNA replication / membrane / metal ion binding
Similarity search - Function
LCP protein / DNA polymerase processivity factor / : / DNA polymerase processivity factor / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZTP / Integral membrane regulatory protein Wzg
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Khai Bui, N. / Hoyland, C.N. / Ogasawara, N. ...Kawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Khai Bui, N. / Hoyland, C.N. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J.
CitationJournal: Embo J. / Year: 2011
Title: A widespread family of bacterial cell wall assembly proteins.
Authors: Kawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Bui, N.K. / Hoyland, C.N. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: CPS2A, Integral membrane regulatory protein Wzg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0938
Polymers43,9971
Non-polymers1,0957
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.348, 73.348, 163.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein CPS2A, Integral membrane regulatory protein Wzg


Mass: 43997.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPC02_0004, wzg / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K376
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZTP / (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl trihydrogen diphosphate


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS ...THE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS DETECTED BY MASS SPECTROSCOPY; THE MASS SPECTROSCOPY DATA DO NOT RULE OUT THE PRESENCE OF OTHER POLYPRENOL PYROPHOSPHATE LIGANDS IN THE SAME BINDING SITE. THE LIGAND HAS BEEN MODELLED WITH THE SEVEN CHIRAL DOUBLE BONDS IN THE CIS CONFIGURATION, AS OCCUR IN THE EQUIVALENT DOUBLE BONDS IN THE LIPID CHAIN OF THE NATURALLY OCCURING SUBSTRATE OF THE ENZYME. THE ELECTRON DENSITY CAN ALSO ACOMMODATE DITRANSPENTACISOCTAPRENYL PYROPHOSPHATE{IUPAC NAME[(2Z,6Z,10Z,14Z,18Z,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL] PHOSPHONOHYDROGEN PHOSPHATE}, AN INTERMEDIATE IN THE SYNTHESIS OF UNDECAPRENYL PYROPHOSPHATE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5 10% PEG 8K 8% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2011
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→19.73 Å / Num. obs: 28883 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.05→2.16 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.515 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24207 1456 5.1 %RANDOM
Rwork0.19058 ---
obs0.19305 27357 99.64 %-
all-28971 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 73 159 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9814042
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56225.669127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9671511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 83 -
Rwork0.201 1787 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: -4.3042 Å / Origin y: -21.5388 Å / Origin z: -14.1745 Å
111213212223313233
T0.0208 Å20.0049 Å2-0.0167 Å2-0.0435 Å2-0.0088 Å2--0.0323 Å2
L0.0707 °20.0432 °2-0.0094 °2-0.6348 °2-0.0848 °2--0.2494 °2
S-0.0101 Å °0.0427 Å °-0.0165 Å °0.0302 Å °-0.024 Å °-0.0845 Å °-0.014 Å °0.0089 Å °0.0341 Å °

+
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