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- PDB-6wvb: Takifugu rubripes VKOR-like with warfarin -

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Basic information

Entry
Database: PDB / ID: 6wvb
TitleTakifugu rubripes VKOR-like with warfarin
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
S-WARFARIN / 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: 2.872 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,0912
Polymers46,7831
Non-polymers3081
Water905
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)65.503, 93.386, 162.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 46782.574 Da / Num. of mol.: 1
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-SWF / S-WARFARIN


Mass: 308.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticoagulant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 5.5 / Details: 23% PEG400, 0.1 M Sodium nitrate, 0.1 M MES pH 5.5

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.872→50 Å / Num. obs: 10896 / % possible obs: 93.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 58.45 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.095 / Rrim(I) all: 0.163 / Χ2: 1.217 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.40.6835350.5210.5060.8551.09793.5
2.95-32.40.6345330.5190.4660.7911.09392.1
3-3.062.40.5855080.5760.4290.731.25490.6
3.06-3.122.40.5045070.7050.3610.6231.10687.3
3.12-3.192.60.4745120.7310.340.5861.36593.1
3.19-3.272.60.3795530.8150.2750.4711.32596.5
3.27-3.352.70.3355600.8170.2440.4161.31394.9
3.35-3.442.60.3165450.8180.2340.3951.27996.3
3.44-3.542.60.2595330.880.1890.3221.24796
3.54-3.652.60.2355570.9110.1680.291.25594.9
3.65-3.782.50.1985300.9430.1420.2451.34792.7
3.78-3.942.60.1675250.9440.120.2071.14390.7
3.94-4.112.80.1265680.9760.090.1561.16396.9
4.11-4.332.70.115580.9830.0780.1361.17297.9
4.33-4.62.50.1155500.9680.0850.1431.37493.7
4.6-4.962.50.0845460.990.060.1031.22594
4.96-5.462.70.0765480.990.0530.0941.20993.5
5.46-6.242.80.0785770.990.0550.0961.13496.5
6.24-7.862.60.0685560.990.0490.0841.09493
7.86-502.70.0495950.9950.0340.0591.16191.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.872→40.513 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 559 5.14 %
Rwork0.2406 10311 -
obs0.2429 10870 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.88 Å2 / Biso mean: 59.972 Å2 / Biso min: 31.13 Å2
Refinement stepCycle: final / Resolution: 2.872→40.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 23 5 3256
Biso mean--60.09 45.56 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033333
X-RAY DIFFRACTIONf_angle_d0.5784514
X-RAY DIFFRACTIONf_chiral_restr0.042510
X-RAY DIFFRACTIONf_plane_restr0.004565
X-RAY DIFFRACTIONf_dihedral_angle_d14.4551955
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8724-3.16140.37691530.3067233686
3.1614-3.61860.3151230.2718263996
3.6186-4.5580.26761490.2294261694
4.558-40.5130.25721340.217272093
Refinement TLS params.Method: refined / Origin x: 75.8144 Å / Origin y: 22.8179 Å / Origin z: 182.6501 Å
111213212223313233
T0.3565 Å2-0.0221 Å2-0.0268 Å2-0.2794 Å2-0.0001 Å2--0.4647 Å2
L0.7345 °2-0.2518 °2-0.0809 °2-0.5015 °20.021 °2--2.738 °2
S-0.0468 Å °-0.0469 Å °-0.01 Å °0.0692 Å °-0.0296 Å °0.0076 Å °-0.0006 Å °-0.1109 Å °0.0598 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 416
2X-RAY DIFFRACTION1allC1 - 5
3X-RAY DIFFRACTION1allB3001

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