[English] 日本語
Yorodumi
- PDB-1bsl: STRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bsl
TitleSTRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN
ComponentsBACTERIAL LUCIFERASE
KeywordsFLAVOPROTEIN / PHOTOPROTEIN / LUMINESCENCE / OXIDOREDUCTASE / MONOOXYGENASE / FMN
Function / homology
Function and homology information


bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / bioluminescence / cytosol
Similarity search - Function
Alkanal monooxygenase / Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel ...Alkanal monooxygenase / Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Alkanal monooxygenase beta chain
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsRayment, I. / Holden, H.M. / Thoden, J.B. / Baldwin, T.O.
Citation
Journal: Protein Sci. / Year: 1997
Title: Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.
Authors: Thoden, J.B. / Holden, H.M. / Fisher, A.J. / Sinclair, J.F. / Wesenberg, G. / Baldwin, T.O. / Rayment, I.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The 1.5-A Resolution Crystal Structure of Bacterial Luciferase in Low Salt Conditions
Authors: Fisher, A.J. / Thompson, T.B. / Thoden, J.B. / Baldwin, T.O. / Rayment, I.
History
DepositionOct 22, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACTERIAL LUCIFERASE
B: BACTERIAL LUCIFERASE


Theoretical massNumber of molelcules
Total (without water)72,7692
Polymers72,7692
Non-polymers00
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.800, 62.000, 218.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BACTERIAL LUCIFERASE


Mass: 36384.684 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07739, bacterial luciferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12.5 mg/mlprotein1drop
250 mMphosphate1drop
30.5 mMEDTA1drop
40.25 mMdithiothreitol1drop
50.75 Mammonium sulfate1drop
6125 mMsodium borate1drop
725 mMsuccinic1drop
81.5 Mammonium sulfate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 55442 / % possible obs: 93.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.041
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. measured all: 125700
Reflection shell
*PLUS
Highest resolution: 1.95 Å / % possible obs: 85.1 % / Num. unique obs: 6873 / Num. measured obs: 9563 / Rmerge(I) obs: 0.18

-
Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 1.95→30 Å /
RfactorNum. reflection
Rwork0.188 -
obs-55442
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 0 989 6116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_deg16.9
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

+
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