[English] 日本語
Yorodumi
- PDB-6rej: Crystal structure of Pizza6-SH with Zn2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rej
TitleCrystal structure of Pizza6-SH with Zn2+
ComponentsPizza6-SH
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Zinc / Pizza / Metalloprotein
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNoguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG0E4717N, G0F9316N, G051917N Belgium
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Artificial beta-propeller protein-based hydrolases.
Authors: Clarke, D.E. / Noguchi, H. / Gryspeerdt, J.A.G. / De Feyter, S. / Voet, A.R.D.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4889
Polymers25,8731
Non-polymers6158
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-217 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.958, 55.179, 69.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pizza6-SH


Mass: 25872.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.77 Å3/Da / Density % sol: 30.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.05M tri-Sodium citrate, 1.2M Ammonium sulfate, 3%(v/w) isopropanol, 10mM ZnSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→47.96 Å / Num. obs: 22795 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.32 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1093

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ww9

3ww9


Resolution: 1.65→39.454 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2358 1140 5.02 %
Rwork0.1933 --
obs0.1955 22730 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→39.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 20 128 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081913
X-RAY DIFFRACTIONf_angle_d0.9132654
X-RAY DIFFRACTIONf_dihedral_angle_d8.971097
X-RAY DIFFRACTIONf_chiral_restr0.288333
X-RAY DIFFRACTIONf_plane_restr0.007353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.72520.34241490.27022638X-RAY DIFFRACTION100
1.7252-1.81620.28661380.23072642X-RAY DIFFRACTION100
1.8162-1.930.24631410.20292665X-RAY DIFFRACTION100
1.93-2.0790.25961310.18922689X-RAY DIFFRACTION100
2.079-2.28820.23781270.18232704X-RAY DIFFRACTION100
2.2882-2.61920.2541360.19632705X-RAY DIFFRACTION100
2.6192-3.29970.23031710.20252691X-RAY DIFFRACTION100
3.2997-39.46520.21271470.17912856X-RAY DIFFRACTION100

+
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