[English] 日本語
Yorodumi
- PDB-6y2t: Streptavidin wildtype with a biotC4-1 cofactor - an artificial ir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y2t
TitleStreptavidin wildtype with a biotC4-1 cofactor - an artificial iron hydroxylase
ComponentsStreptavidin
KeywordsOXIDOREDUCTASE / Artificial Metalloenzyme / Iron Hydroxylase / Biotin-Binding Protein
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
biotC4-1 cofactor / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSerrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R.
Funding support Switzerland, European Union, Germany, 5items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_182046 Switzerland
Swiss National Science FoundationNCCR MSE Switzerland
European Research Council (ERC)694424European Union
European Molecular Biology Organization (EMBO)ALTF 194-2017 Germany
European Research Council (ERC)H2020-MSCA-IF-2016European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Enantioselective Hydroxylation of Benzylic C(sp3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology.
Authors: Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0885
Polymers16,5691
Non-polymers1,5194
Water1,820101
1
AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules

AAA: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,35320
Polymers66,2764
Non-polymers6,07716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12660 Å2
ΔGint-55 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.714, 57.714, 184.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11AAA-327-

HOH

-
Components

#1: Protein Streptavidin /


Mass: 16569.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P22629
#2: Chemical ChemComp-O6T / biotC4-1 cofactor


Mass: 667.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H37FeN7O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→46.076 Å / Num. obs: 23212 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.704 / Num. unique obs: 1135 / CC1/2: 0.793 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PK2
Resolution: 1.55→46.076 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2004 1161 5.009 %
Rwork0.1688 --
all0.17 --
obs-23178 99.931 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 100 101 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131065
X-RAY DIFFRACTIONr_bond_other_d0.0380.018827
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.8011493
X-RAY DIFFRACTIONr_angle_other_deg2.5141.5721909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.22622.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95415128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.562154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021158
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02220
X-RAY DIFFRACTIONr_nbd_refined0.2080.2160
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.2725
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2486
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.225
X-RAY DIFFRACTIONr_nbd_other0.2390.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.217
X-RAY DIFFRACTIONr_mcbond_it2.2912.305500
X-RAY DIFFRACTIONr_mcbond_other2.1882.302499
X-RAY DIFFRACTIONr_mcangle_it3.2483.448629
X-RAY DIFFRACTIONr_mcangle_other3.2543.452630
X-RAY DIFFRACTIONr_scbond_it3.3082.725563
X-RAY DIFFRACTIONr_scbond_other3.3052.729564
X-RAY DIFFRACTIONr_scangle_it4.7643.993859
X-RAY DIFFRACTIONr_scangle_other4.7613.999860
X-RAY DIFFRACTIONr_lrange_it6.55828.7541145
X-RAY DIFFRACTIONr_lrange_other6.53128.4541133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.228840.2281586X-RAY DIFFRACTION100
1.59-1.6340.231830.2121571X-RAY DIFFRACTION100
1.634-1.6810.215790.1891498X-RAY DIFFRACTION100
1.681-1.7330.239770.2031477X-RAY DIFFRACTION100
1.733-1.790.215760.1651433X-RAY DIFFRACTION99.9338
1.79-1.8520.163730.1511383X-RAY DIFFRACTION100
1.852-1.9220.169700.1621337X-RAY DIFFRACTION99.5754
1.922-2.0010.166670.1591283X-RAY DIFFRACTION99.926
2.001-2.090.228660.1651250X-RAY DIFFRACTION100
2.09-2.1920.197630.1541190X-RAY DIFFRACTION100
2.192-2.310.175600.1561146X-RAY DIFFRACTION100
2.31-2.450.205560.151061X-RAY DIFFRACTION100
2.45-2.6190.157540.1451024X-RAY DIFFRACTION100
2.619-2.8290.192500.162947X-RAY DIFFRACTION100
2.829-3.0990.222470.156882X-RAY DIFFRACTION100
3.099-3.4640.193420.167802X-RAY DIFFRACTION99.8817
3.464-3.9990.157380.15719X-RAY DIFFRACTION100
3.999-4.8950.169330.136623X-RAY DIFFRACTION100
4.895-6.9130.227260.203497X-RAY DIFFRACTION100
6.913-46.0760.338170.314308X-RAY DIFFRACTION99.6933

+
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