[English] 日本語
Yorodumi
- PDB-7snr: 2.00A Resolution Structure of NanoLuc Luciferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7snr
Title2.00A Resolution Structure of NanoLuc Luciferase
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / Selenomethionine
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / ACETATE ION / CITRATE ANION / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: 2.00A Resolution Structure of NanoLuc Luciferase
Authors: Encell, L.P. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Wood, K.V.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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)39,4475
Polymers39,1402
Non-polymers3073
Water2,720151
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8774
Polymers19,5701
Non-polymers3073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)19,5701
Polymers19,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.188, 55.800, 55.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

-
Components

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


Mass: 19569.850 Da / Num. of mol.: 2
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 KRX (bacteria)
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.68 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0 M ammonium citrate dibasic, 0.1 M sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.06 Å / Num. obs: 28770 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.046 / Rrim(I) all: 0.167 / Net I/σ(I): 14.3 / Num. measured all: 378302
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0513.51.3042782820620.7560.3671.3552.3100
8.94-44.0611.40.05444003870.9990.0160.0565098.7

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
SHELXphasing
PHENIXdev_4289refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→42.71 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 2742 5.08 %
Rwork0.1839 51253 -
obs0.1854 28770 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.87 Å2 / Biso mean: 34.7703 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 21 151 2669
Biso mean--26.23 33.72 -
Num. residues----322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.030.29141390.252225092648
2.03-2.070.30291360.25625932729
2.07-2.110.3141200.233925692689
2.11-2.150.27431470.22725692716
2.15-2.20.25191270.210125472674
2.2-2.250.20561200.193525942714
2.25-2.310.25721380.201325682706
2.31-2.370.26221410.19525492690
2.37-2.440.24671390.197625622701
2.44-2.520.21641370.182125732710
2.52-2.610.23231020.194626022704
2.61-2.710.24171320.177825882720
2.71-2.840.28171330.188225622695
2.84-2.990.2381580.190225412699
2.99-3.170.22851350.180825512686
3.17-3.420.20261570.160725452702
3.42-3.760.18381210.168926032724
3.76-4.310.13971700.146725312701
4.31-5.420.1591700.144225112681
5.43-42.710.2481200.223825862706
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)
10.17780.07430.10690.0776-0.02650.08640.00410.0375-0.07210.0122-0.02250.0971-0.0203-0.0138-0.00020.1841-0.02090.03060.14-0.00440.1494124.64537.61437.427
20.07670.05120.00170.1074-0.06880.05980.14530.0070.179-0.1599-0.1004-0.0435-0.253-0.04450.00010.21680.02170.0380.1542-0.02020.1941131.18340.63738.534
30.27840.36460.2720.55270.2370.27170.01140.03360.07940.06020.0805-0.1326-0.06380.0260.00590.1735-0.00520.03340.1359-0.01430.2193133.64344.45336.675
40.10310.07640.03630.05140.02130.0344-0.02990.00060.1375-0.01750.03430.09790.0099-0.2192-00.1781-0.01240.02260.16040.01190.1618120.47638.38636.104
50.13420.0980.16520.11620.05540.39540.0467-0.15020.2334-0.1556-0.15860.0738-0.1091-0.6368-0.01170.3192-0.02350.0080.3867-0.02340.312108.95634.63615.262
60.2453-0.0911-0.19290.2785-0.04450.1764-0.024-0.62530.29590.0094-0.22140.20990.0846-0.5456-0.5224-0.07940.02110.08820.9127-0.28410.32295.47739.2613.514
70.00130.04320.04280.10210.20790.29820.04190.08240.070.0459-0.0934-0.0978-0.2208-0.2227-0.00060.23350.02580.00830.26540.02860.1778113.12538.58110.426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:26 )A2 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:52 )A27 - 52
3X-RAY DIFFRACTION3( CHAIN A AND RESID 53:132 )A53 - 132
4X-RAY DIFFRACTION4( CHAIN A AND RESID 133:168 )A133 - 168
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:52 )B1 - 52
6X-RAY DIFFRACTION6( CHAIN B AND RESID 53:100 )B53 - 100
7X-RAY DIFFRACTION7( CHAIN B AND RESID 101:168 )B101 - 168

+
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