[English] 日本語
Yorodumi
- PDB-2d1s: Crystal structure of the thermostable Japanese Firefly Luciferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d1s
TitleCrystal structure of the thermostable Japanese Firefly Luciferase complexed with High-energy intermediate analogue
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE / ALPHA/BETA / BETA BARREL / ALPHA+BETA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesLuciola cruciata (Japanese firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsNakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nature / Year: 2006
Title: Structural basis for the spectral difference in luciferase bioluminescence.
Authors: Nakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H.
History
DepositionAug 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7954
Polymers60,1171
Non-polymers6783
Water14,304794
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.586, 181.313, 52.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 60117.156 Da / Num. of mol.: 1 / Mutation: T217I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Luciola cruciata (Japanese firefly) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P13129, firefly luciferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SLU / 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE


Mass: 606.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N8O8S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8
Details: PEG4000, Lithium chrolide, Magnesium chloride, HEPES, 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine, pH 7.8, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 8, 2002
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.3→60 Å / Num. all: 133611 / Num. obs: 133611 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 2.6 / Num. unique all: 12734 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2D1Q

2d1q


Resolution: 1.3→60 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.728 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 6710 5 %RANDOM
Rwork0.18011 ---
all0.18115 133504 --
obs0.18115 126794 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4127 0 42 794 4963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224254
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9885774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075538
X-RAY DIFFRACTIONr_chiral_restr0.120.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023137
X-RAY DIFFRACTIONr_nbd_refined0.1970.22095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2579
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.236
X-RAY DIFFRACTIONr_mcbond_it0.6391.52672
X-RAY DIFFRACTIONr_mcangle_it1.16224344
X-RAY DIFFRACTIONr_scbond_it1.76731582
X-RAY DIFFRACTIONr_scangle_it2.7954.51430
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 489
Rwork0.298 8843

+
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