[English] 日本語
Yorodumi
- PDB-2psh: Crystal Structures of the Luciferase and Green Fluorescent Protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2psh
TitleCrystal Structures of the Luciferase and Green Fluorescent Protein from Renilla Reniformis
ComponentsRenilla-luciferin 2-monooxygenase
KeywordsOXIDOREDUCTASE / alpha/beta-hydrolase / luciferase
Function / homology
Function and homology information


Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / epoxide hydrolase activity / carboxy-lyase activity / bioluminescence
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsLoening, A.M. / Fenn, T.D. / Gambhir, S.S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of the Luciferase and Green Fluorescent Protein from Renilla reniformis.
Authors: Loening, A.M. / Fenn, T.D. / Gambhir, S.S.
History
DepositionMay 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Renilla-luciferin 2-monooxygenase
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)74,0302
Polymers74,0302
Non-polymers00
Water8,575476
1
A: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)37,0151
Polymers37,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)37,0151
Polymers37,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.776, 75.652, 89.185
Angle α, β, γ (deg.)90.00, 76.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 310 / Label seq-ID: 3 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Renilla-luciferin 2-monooxygenase / Renilla-type luciferase


Mass: 37015.230 Da / Num. of mol.: 2
Mutation: T2A, K25A, A55T, C124A, S130A, K136R, A143M, M185V, M253L, E277A, S287L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Gene: rluc / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P27652, Renilla-type luciferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1~M HEPES, 10% v/v isopropanol with 6mg/ml benzyl-coelenterazine, 15% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.79→100 Å / Num. obs: 58344 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→86.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.928 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22941 3119 5.1 %RANDOM
Rwork0.19523 ---
obs0.19698 58344 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.04 Å2
2--0.13 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.79→86.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 0 476 5336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224994
X-RAY DIFFRACTIONr_bond_other_d0.0010.023487
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9526755
X-RAY DIFFRACTIONr_angle_other_deg0.87838473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.824238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8971528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2120.21072
X-RAY DIFFRACTIONr_nbd_other0.1930.23548
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22446
X-RAY DIFFRACTIONr_nbtor_other0.0820.22337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2379
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.53864
X-RAY DIFFRACTIONr_mcbond_other0.1221.51192
X-RAY DIFFRACTIONr_mcangle_it0.85824821
X-RAY DIFFRACTIONr_scbond_it1.39532434
X-RAY DIFFRACTIONr_scangle_it1.9944.51934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4149 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.42 Å

TypeWeight position
medium positional0.5
medium thermal2
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 201 -
Rwork0.298 3552 -
obs--80.69 %

+
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