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- PDB-6wv4: Human VKOR C43S with warfarin -

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Basic information

Entry
Database: PDB / ID: 6wv4
TitleHuman VKOR C43S with warfarin
ComponentsVitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / vitamin K expoxide(KO) / membrane protein
Function / homology
Function and homology information


peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / quinone binding / xenobiotic metabolic process / bioluminescence ...peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / quinone binding / xenobiotic metabolic process / bioluminescence / generation of precursor metabolites and energy / bone development / blood coagulation / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum
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
S-WARFARIN / Green fluorescent protein / Green fluorescent protein / Vitamin K epoxide reductase complex subunit 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.012 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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
Revision 1.5Nov 13, 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 Cys43Ser mutant, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4902
Polymers44,1811
Non-polymers3081
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint1 kcal/mol
Surface area18040 Å2
Unit cell
Length a, b, c (Å)43.299, 49.346, 288.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein / Vitamin K1 2 / 3-epoxide reductase subunit 1


Mass: 44181.371 Da / Num. of mol.: 1
Fragment: GPF (UNP residues 1-144) + VKOR + GFP (UNP residues 146-231)
Mutation: C43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: gfp, VKORC1, VKOR, MSTP134, MSTP576, UNQ308/PRO351 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A059PIQ0, UniProt: Q9BQB6, UniProt: P42212*PLUS, vitamin-K-epoxide reductase (warfarin-sensitive)
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 25-33% PEG400, 185-220 mM potassium formate, 0.1 M MES, pH 6.5

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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 PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.01→49.35 Å / Num. obs: 11474 / % possible obs: 90 % / Redundancy: 4.5 % / Biso Wilson estimate: 13.83 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.143 / Rrim(I) all: 0.309 / Net I/σ(I): 4.6 / Num. measured all: 51175 / Scaling rejects: 22
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
3.01-3.194.41.309768317630.2010.7131.5021.388.4
9.03-49.354.10.06518884640.9970.0350.07413.885.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 3.012→48.641 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.17
RfactorNum. reflection% reflection
Rfree0.2921 563 5.01 %
Rwork0.2694 --
obs0.2704 11227 86.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.63 Å2 / Biso mean: 74.4269 Å2 / Biso min: 21.67 Å2
Refinement stepCycle: final / Resolution: 3.012→48.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 0 8 2884
Biso mean---43.18 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052968
X-RAY DIFFRACTIONf_angle_d0.6844018
X-RAY DIFFRACTIONf_chiral_restr0.044450
X-RAY DIFFRACTIONf_plane_restr0.004502
X-RAY DIFFRACTIONf_dihedral_angle_d16.0751716
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.012-3.31460.35161350.3356247782
3.3146-3.7940.34381380.3072270089
3.794-4.77940.27611430.2437270588
4.7794-48.6410.2581470.2486278285
Refinement TLS params.Method: refined / Origin x: 13.8157 Å / Origin y: -16.8792 Å / Origin z: -45.1281 Å
111213212223313233
T0.2185 Å20.0335 Å20.0173 Å2-0.2463 Å2-0.0594 Å2--0.2505 Å2
L0.0504 °20.0136 °2-0.0485 °2--0.0244 °2-0.0169 °2--0.0369 °2
S-0.0415 Å °-0.0753 Å °-0.0228 Å °-0.04 Å °0.0281 Å °0.0415 Å °0.1282 Å °0.0168 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 381
2X-RAY DIFFRACTION1allC3001
3X-RAY DIFFRACTION1allB1 - 14

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