[English] 日本語
Yorodumi
- PDB-4n1f: Crystal Structure of F88Y obelin mutant from Obelia longissima at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n1f
TitleCrystal Structure of F88Y obelin mutant from Obelia longissima at 2.09 Angstrom resolution
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / calcium binding / EF-hand
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
EF hand / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF hand / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
C2-HYDROPEROXY-COELENTERAZINE / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.087 Å
AuthorsNatashin, P.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structures of the F88Y obelin mutant before and after bioluminescence provide molecular insight into spectral tuning among hydromedusan photoproteins
Authors: Natashin, P.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 8, 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 / 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: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7102
Polymers22,2551
Non-polymers4551
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.329, 73.329, 53.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Obelin / OBL


Mass: 22254.904 Da / Num. of mol.: 1 / Mutation: S2A, F88Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold / References: UniProt: Q27709
#2: Chemical ChemComp-CZH / C2-HYDROPEROXY-COELENTERAZINE / 8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE


Mass: 455.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.087→50 Å / Num. all: 16926 / Num. obs: 16926 / % possible obs: 99.88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.51 Å2
Reflection shellResolution: 2.09→2.16 Å / % possible all: 99.12

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QV0

1qv0


Resolution: 2.087→42.996 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.18 / σ(F): 1.37 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 1691 10 %RANDOM
Rwork0.1716 ---
all0.2163 16908 --
obs0.1744 16906 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.39 Å2 / Biso mean: 41.7928 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: LAST / Resolution: 2.087→42.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 34 164 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051593
X-RAY DIFFRACTIONf_angle_d0.8762161
X-RAY DIFFRACTIONf_chiral_restr0.067218
X-RAY DIFFRACTIONf_plane_restr0.003281
X-RAY DIFFRACTIONf_dihedral_angle_d14.877583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0873-2.14870.26971420.21161256139899
2.1487-2.21810.23861470.20112581405100
2.2181-2.29740.25041380.189912561394100
2.2974-2.38930.18351380.184612561394100
2.3893-2.49810.21241410.17712561397100
2.4981-2.62970.21481380.189112701408100
2.6297-2.79450.24661450.187412571402100
2.7945-3.01020.19861380.197112661404100
3.0102-3.3130.23971470.191512761423100
3.313-3.79220.21181330.155912701403100
3.7922-4.77670.15511440.144312781422100
4.7767-43.00540.1661400.159413161456100
Refinement TLS params.Method: refined / Origin x: 69.5298 Å / Origin y: 24.4798 Å / Origin z: 25.6833 Å
111213212223313233
T0.3161 Å2-0.0363 Å20.081 Å2-0.2127 Å20.0284 Å2--0.2345 Å2
L2.926 °2-0.3594 °20.0271 °2-4.6597 °2-0.2476 °2--2.3955 °2
S-0.1043 Å °0.2657 Å °0.0858 Å °-0.1255 Å °0.2975 Å °0.3126 Å °-0.3228 Å °-0.0934 Å °-0.1853 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://pdbjlc1.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