[English] 日本語
Yorodumi
- PDB-5ibo: 1.95A resolution structure of NanoLuc luciferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ibo
Title1.95A resolution structure of NanoLuc luciferase
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / Oplophorus bioluminescent protein / NanoLuc luciferase / NLuc / coelenterazine / furimazine / beta-barrel
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / DECANOIC ACID / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
CitationJournal: To be published
Title: To be determined
Authors: Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2034
Polymers38,8582
Non-polymers3452
Water1,26170
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,4291
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,4291
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.436, 62.658, 96.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Oplophorus-luciferin 2-monooxygenase catalytic subunit / 19kOLase


Mass: 19429.164 Da / Num. of mol.: 2 / Fragment: Full Length
Mutation: A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Plasmid: pFN18K(-AIA) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200 mM ammonium nitrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.42 Å / Num. obs: 27490 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 17.4 / Num. measured all: 171068 / Scaling rejects: 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-26.10.8561100
8.94-48.425.60.02199.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.18 Å48.42 Å
Translation3.12 Å48.42 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
Aimless0.1.29data scaling
PHASER2.5.4phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house Selenomethionine Structure

Resolution: 1.95→48.417 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1325 5.04 %
Rwork0.1883 --
obs0.1913 26285 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→48.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 24 70 2670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122650
X-RAY DIFFRACTIONf_angle_d1.0983596
X-RAY DIFFRACTIONf_dihedral_angle_d13.6811528
X-RAY DIFFRACTIONf_chiral_restr0.071418
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.02820.31441210.24172630X-RAY DIFFRACTION92
2.0282-2.12050.27471560.22922832X-RAY DIFFRACTION100
2.1205-2.23230.23181560.20262751X-RAY DIFFRACTION96
2.2323-2.37220.23271450.1992482X-RAY DIFFRACTION88
2.3722-2.55530.29841340.21152655X-RAY DIFFRACTION92
2.5553-2.81240.28651540.21262787X-RAY DIFFRACTION97
2.8124-3.21930.26411510.19772880X-RAY DIFFRACTION99
3.2193-4.05570.24641590.16892902X-RAY DIFFRACTION99
4.0557-48.43240.21551490.16493041X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09390.0547-0.00120.1853-0.14350.116-0.06570.1670.09340.08520.0614-0.0917-0.0783-0.0847-0.09310.07980.04670.02310.16920.04440.153455.535943.890312.8522
20.0079-0.0177-0.0110.16810.11130.0771-0.00890.26690.07010.03750.09410.26250.0888-0.05520.06050.1130.01130.04450.23090.05140.248645.642234.915912.7416
30.02350.1213-0.08270.6827-0.25770.1431-0.08450.11130.21910.30460.0147-0.0151-0.22710.0011-0.01880.03510.0355-0.01510.22350.04840.179657.401548.34436.8032
40.136-0.0961-0.0410.21250.23020.3492-0.03480.10990.13290.1755-0.06480.05-0.0372-0.1267-0.16750.55580.07980.0790.12170.03810.253745.882335.986135.2016
50.0063-0.0014-0.00120.0007-0.00120.0018-0.0025-0.022-0.08080.01510.00630.00150.0357-0.0007-00.43250.03470.0480.23670.06480.34551.878650.646229.6939
60.2457-0.04740.1030.0919-0.08780.09750.0442-0.04430.09830.28260.03460.07610.14170.08360.00620.57130.01740.00370.19650.02780.205257.264138.122138.1341
70.0974-0.08920.0480.144-0.05960.04460.1052-0.13290.14950.56570.05570.02490.18390.06190.07720.7850.03250.08620.0975-0.03620.270357.270145.87440.4993
80.10260.04520.07630.16440.20730.48770.0245-0.01240.16420.60890.09940.1844-0.4003-0.1060.25620.87620.12010.35090.0436-0.16770.076442.818837.345839.6278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 169 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 113 )
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 169 )

+
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