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- PDB-6wva: Takifugu rubripes VKOR-like with vitamin K1 epoxide at non-cataly... -

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Basic information

Entry
Database: PDB / ID: 6wva
TitleTakifugu rubripes VKOR-like with vitamin K1 epoxide at non-catalytic state
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 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein ...Vitamin K epoxide reductase complex subunit 1 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Green fluorescent protein / Vitamin K epoxide reductase complex subunit 1-like protein 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Takifugu rubripes (torafugu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 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
CitationJournal: 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.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)46,7831
Polymers46,7831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.416, 49.217, 84.236
Angle α, β, γ (deg.)90.000, 112.400, 90.000
Int Tables number5
Space group name H-MC121

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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.) Aequorea victoria (jellyfish), (gene. exp.) Takifugu rubripes (torafugu)
Gene: GFP, Vkorc1l1 / Production host: Komagataella pastoris (fungus)
References: UniProt: P42212, UniProt: Q6TEK8, vitamin-K-epoxide reductase (warfarin-sensitive)
Has ligand of interestN
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 7.5
Details: 42% PEG 400, 50 mM ammonium formate, 0.1 M HEPES pH 7.5

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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: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 10574 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 85.44 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.075 / Rrim(I) all: 0.147 / Χ2: 1.207 / Net I/σ(I): 7.5 / Num. measured all: 38881
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.153.61.085030.6580.6481.2651.09498.8
3.15-3.213.80.7875330.6750.4520.9121.13699.1
3.21-3.273.80.7585250.6920.4380.8791.04899.1
3.27-3.343.70.6365260.870.3820.7451.06998.3
3.34-3.413.70.4965260.860.2930.5781.16699.4
3.41-3.493.80.4315400.8970.2510.5021.2398
3.49-3.583.70.365080.9090.2120.421.20198.8
3.58-3.683.60.3175280.9110.1890.3711.17798.9
3.68-3.783.40.2445210.9370.1480.2871.11996.1
3.78-3.913.60.2125200.960.1260.2481.27998.1
3.91-4.0440.1725470.9740.0990.1991.19798.9
4.04-4.213.90.1465210.9840.0840.1691.16898.7
4.21-4.43.70.195170.980.1110.2211.78599
4.4-4.633.40.1165340.9780.0710.1371.84196.7
4.63-4.923.60.0925260.9890.0550.1081.22998
4.92-5.33.60.085290.9920.0480.0941.19198
5.3-5.833.90.0825360.9880.0470.0951.12599.1
5.83-6.673.80.0785350.990.0460.0911.00998.7
6.67-8.43.50.0685430.9920.040.0791.04797.5
8.4-503.50.0575560.9960.0350.0671.1296

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 3.35→42.32 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 407 4.84 %
Rwork0.2243 7997 -
obs0.2268 8404 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.22 Å2 / Biso mean: 95.2142 Å2 / Biso min: 29.1 Å2
Refinement stepCycle: final / Resolution: 3.35→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 0 3256
Num. residues----412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.830.31671400.26032626276698
3.83-4.830.31561410.24172633277497
4.83-42.320.23011260.19872738286498

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