[English] 日本語
Yorodumi
- PDB-4zin: Genetically encoded Phenyl Azide Photochemistry Drive Positive an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zin
TitleGenetically encoded Phenyl Azide Photochemistry Drive Positive and Negative Functional Modulation of a Red Fluorescent Protein
ComponentsMCherry fluorescent protein
KeywordsFLUORESCENT PROTEIN / mCherry / Photoactivation / Photodeactivation / Coloration / Fluorescence / Microscopy / Phenyl Azide / Non-canonical amino acids / Optogenetics / Synchrotron
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MCherry fluorescent protein
Similarity search - Component
Biological speciesAnaplasma marginale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsReddington, S.C. / Driezis, S. / Hartley, A.M. / Watson, P.D. / Rizkallah, P.J. / Jones, D.D.
CitationJournal: Rsc Adv / Year: 2015
Title: Genetically encoded phenyl azide photochemistry drives positive and negative functional modulation of a red fluorescent protein
Authors: Reddington, S.C. / Driezis, S. / Hartley, A.M. / Watson, P.D. / Rizkallah, P.J. / Jones, D.D.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Oct 23, 2019Group: Data collection / Database references
Category: citation / pdbx_database_related / struct_ref_seq_dif
Item: _citation.page_last / _struct_ref_seq_dif.details
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.mon_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_comp_id / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MCherry fluorescent protein
B: MCherry fluorescent protein
C: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,98410
Polymers74,3463
Non-polymers6387
Water7,206400
1
A: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9743
Polymers24,7821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9743
Polymers24,7821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0364
Polymers24,7821
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.280, 103.430, 150.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MCherry fluorescent protein


Mass: 24781.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma marginale (bacteria) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8 / Details: Sitting drop / PH range: 7.9-8.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.67→51.71 Å / Num. obs: 79561 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Net I/σ(I): 13.6 / Num. measured all: 567722
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.67-1.717.20.8142.44145857700.7720.324100
7.47-51.716.40.03830.6659610240.9970.01699.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.77 Å51.72 Å
Translation4.77 Å51.72 Å

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5O

2h5o


Resolution: 1.67→51.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2562 / WRfactor Rwork: 0.2102 / FOM work R set: 0.7972 / SU B: 5.909 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1144 / SU Rfree: 0.1152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3874 4.9 %RANDOM
Rwork0.2059 ---
obs0.208 75603 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.2 Å2 / Biso mean: 29.43 Å2 / Biso min: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20 Å2
2--0.01 Å20 Å2
3---2.37 Å2
Refinement stepCycle: final / Resolution: 1.67→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 34 400 5669
Biso mean--58.63 37.11 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195394
X-RAY DIFFRACTIONr_bond_other_d0.0010.025027
X-RAY DIFFRACTIONr_angle_refined_deg2.121.9857241
X-RAY DIFFRACTIONr_angle_other_deg0.925311660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0975642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86924.699249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84115945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3581524
X-RAY DIFFRACTIONr_chiral_restr0.140.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215994
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021203
X-RAY DIFFRACTIONr_mcbond_it1.8391.932586
X-RAY DIFFRACTIONr_mcbond_other1.8291.9292585
X-RAY DIFFRACTIONr_mcangle_it2.4712.8873222
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 257 -
Rwork0.285 5508 -
all-5765 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.0184 Å / Origin y: -6.618 Å / Origin z: -33.0201 Å
111213212223313233
T0.1084 Å20.023 Å20.0202 Å2-0.0429 Å20.0081 Å2--0.0072 Å2
L0.1733 °20.0747 °20.0516 °2-0.3625 °2-0.1267 °2--0.0836 °2
S0.0066 Å °0.0699 Å °0.0131 Å °-0.0284 Å °0.0015 Å °0.0283 Å °0.005 Å °0.0316 Å °-0.0081 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 300
2X-RAY DIFFRACTION1B1 - 300
3X-RAY DIFFRACTION1C1 - 300

+
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://pdbjlvh1.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