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- PDB-6wv8: Takifugu rubripes VKOR-like C138S mutant with vitamin K1 -

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Basic information

Entry
Database: PDB / ID: 6wv8
TitleTakifugu rubripes VKOR-like C138S mutant with vitamin K1
ComponentsVitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
KeywordsMEMBRANE PROTEIN / Vitamin K epoxide Reductase / VKOR / VKOR-like protein / VKORL
Function / homology
Function and homology information


vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / quinone binding / bioluminescence / generation of precursor metabolites and energy / endoplasmic reticulum membrane
Similarity search - Function
Vitamin K epoxide reductase complex subunit 1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
PHYLLOQUINONE / Green fluorescent protein / Green fluorescent protein / Green fluorescent protein / Vitamin K epoxide reductase complex subunit 1-like protein 1
Similarity search - Component
Biological speciesEscherichia virus RB43
Takifugu rubripes (torafugu)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLiu, S. / Sukumar, N. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Citation
Journal: Science / Year: 2021
Title: Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
Authors: Liu, S. / Li, S. / Shen, G. / Sukumar, N. / Krezel, A.M. / Li, W.
#1: Journal: To Be Published
Title: Termini restraining of small membrane proteins enables structure determination at atomic resolution
Authors: Liu, S. / Li, S. / Yang, Y. / Li, W.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2172
Polymers46,7671
Non-polymers4511
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.167, 61.490, 167.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein


Mass: 46766.512 Da / Num. of mol.: 1 / Mutation: C138S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus RB43, (gene. exp.) Takifugu rubripes (torafugu), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Vkorc1l1, gfp / Production host: Komagataella pastoris (fungus)
References: UniProt: K0NYR4, UniProt: Q6TEK8, UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6
Details: 25% PEG 400, 300 mM ammonium fluoride, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10986 / % possible obs: 93.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.091 / Rrim(I) all: 0.159 / Χ2: 1.102 / Net I/σ(I): 6.9 / Num. measured all: 30113
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.052.80.695620.4130.4870.851.05398.9
3.05-3.112.80.6075640.7920.4330.7491.06799.1
3.11-3.172.80.5435520.5920.380.6671.05698.6
3.17-3.232.70.4335680.6680.3090.5350.96897.4
3.23-3.32.80.4085420.7250.2860.5011.06497
3.3-3.382.60.3655750.7690.2590.451.10497.6
3.38-3.462.60.2865330.8570.2080.3560.99496
3.46-3.562.40.2655520.8920.1940.331.26393.9
3.56-3.662.50.1995080.940.140.2451.20190.4
3.66-3.782.80.2295640.8920.1610.2811.09198.3
3.78-3.912.90.1885820.9450.1280.2281.19399.3
3.91-4.0730.1475790.9630.10.1781.07998.8
4.07-4.262.80.1135610.9780.0790.1381.12798.8
4.26-4.482.50.1014340.9790.0710.1241.1774.3
4.48-4.762.70.0814350.9860.0570.11.11773
4.76-5.132.70.0755540.9880.0530.0921.16294.2
5.13-5.642.60.0745460.990.0530.0911.11791.6
5.64-6.463.10.0755770.9880.0490.091.05597.6
6.46-8.132.90.0526000.9950.0350.0631.06697.2
8.13-502.70.0455980.9960.0310.0551.16988.3

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 3.01→34.57 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2927 570 5.2 %
Rwork0.2553 10383 -
obs0.2573 10953 92.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.73 Å2 / Biso mean: 75.4541 Å2 / Biso min: 38.55 Å2
Refinement stepCycle: final / Resolution: 3.01→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 28 7 3155
Biso mean--72.68 59.91 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.310.33141220.31342487260990
3.31-3.790.32021440.26812642278695
3.79-4.770.28921570.24372476263389
4.77-34.570.27311470.2392778292594
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)
15.0862-2.07780.49414.602-0.47733.6953-0.0939-0.0724-0.3286-0.31070.07930.28630.3641-0.04180.02260.3587-0.05520.01130.1881-0.01150.348658.8765-1.56332.2434
23.62491.53690.73072.56630.2495.282-0.11090.85680.1145-0.8804-0.04230.1381-0.20720.48380.16310.6943-0.039-0.02690.6320.05080.48669.5201-0.643449.3097
33.615-3.33640.25894.8023-1.04040.9232-0.077-0.38850.18580.20960.0197-0.44720.22130.09460.09220.3481-0.0321-0.04510.3222-0.06160.321759.2087.40277.831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 150 )A1 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 299 )A151 - 299
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 407 )A300 - 407

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