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- PDB-7vsx: Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L... -

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Basic information

Entry
Database: PDB / ID: 7vsx
TitleCrystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L18Q and V27L)
ComponentsQLnK
KeywordsLUMINESCENT PROTEIN / mutated 19 kDa protein / Oplophorus luciferase
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.698 Å
AuthorsTomabechi, Y. / Sekine, S. / Shirouzu, M. / Takamitsu, H. / Satoshi, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos One / Year: 2022
Title: Reverse mutants of the catalytic 19 kDa mutant protein (nanoKAZ/nanoLuc) from Oplophorus luciferase with coelenterazine as preferred substrate.
Authors: Inouye, S. / Sato, J.I. / Sahara-Miura, Y. / Tomabechi, Y. / Sumida, Y. / Sekine, S.I. / Shirouzu, M. / Hosoya, T.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: QLnK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3832
Polymers19,1881
Non-polymers1951
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area8810 Å2
Unit cell
Length a, b, c (Å)60.810, 76.000, 103.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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Components

#1: Protein QLnK


Mass: 19187.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES (pH6.5) 1.8-1.9 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.698→47.482 Å / Num. obs: 26866 / % possible obs: 99.7 % / Redundancy: 7.319 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Χ2: 0.976 / Net I/σ(I): 15.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.87.2150.8872.2430383427342110.9360.95698.5
1.8-1.937.3640.4514.3529898406240600.9760.485100
1.93-2.087.3560.2228.0327704376637660.9920.239100
2.08-2.287.3830.13412.8425709348434820.9950.14599.9
2.28-2.557.3910.09517.723379316331630.9960.102100
2.55-2.947.3930.06923.9520746280828060.9970.07499.9
2.94-3.597.3510.05531.2817568239123900.9970.059100
3.59-5.077.2580.05135.4513682188718850.9980.05599.9
5.07-47.4826.8480.0534.747553110711030.9970.05499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å47.48 Å
Translation1.7 Å47.48 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B0U

5b0u


Resolution: 1.698→47.482 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 1996 7.46 %
Rwork0.1817 24756 -
obs0.1836 26752 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.32 Å2 / Biso mean: 37.6905 Å2 / Biso min: 19.22 Å2
Refinement stepCycle: final / Resolution: 1.698→47.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 12 174 1541
Biso mean--47.01 44.84 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141397
X-RAY DIFFRACTIONf_angle_d1.2961896
X-RAY DIFFRACTIONf_chiral_restr0.097212
X-RAY DIFFRACTIONf_plane_restr0.009242
X-RAY DIFFRACTIONf_dihedral_angle_d16.681806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6982-1.74070.43761370.4023168895
1.7407-1.78770.35591380.3176170899
1.7877-1.84030.28161410.2581173299
1.8403-1.89980.26181420.227176699
1.8998-1.96770.27221380.1995172599
1.9677-2.04640.23861430.1941760100
2.0464-2.13960.21481410.20031754100
2.1396-2.25240.221420.1961768100
2.2524-2.39350.22871430.18261775100
2.3935-2.57830.23011430.18821774100
2.5783-2.83770.19221440.18521791100
2.8377-3.24830.22681460.18241801100
3.2483-4.09210.17041440.15531811100
4.0921-4.74820.17191540.16021903100

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