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- PDB-6wv5: Human VKOR C43S mutant with vitamin K1 epoxide -

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Basic information

Entry
Database: PDB / ID: 6wv5
TitleHuman VKOR C43S mutant with vitamin K1 epoxide
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
Chem-UAV / 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: 2.8 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 1.5Oct 23, 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)44,6502
Polymers44,1811
Non-polymers4691
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18690 Å2
Unit cell
Length a, b, c (Å)88.927, 88.927, 229.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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-UAV / (2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione


Mass: 468.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C31H48O3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.96 Å3/Da / Density % sol: 68.94 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 25% PEG400, 0.1 M ammonium citrate dibasic, 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: Jul 15, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15792 / % possible obs: 94.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 57.98 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.056 / Rrim(I) all: 0.095 / Χ2: 1.19 / Net I/σ(I): 9.5 / Num. measured all: 35949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.20.4257840.7520.3340.5451.05896.8
2.85-2.92.30.388010.7950.2890.4820.96495.5
2.9-2.962.20.3637920.8220.280.4631.10994.7
2.96-3.022.30.2817550.8930.2090.3541.19491.7
3.02-3.082.10.2437750.9060.1750.3031.37988.6
3.08-3.152.30.2437900.9030.1810.3061.35195.5
3.15-3.232.30.1998130.9270.150.2511.26797.2
3.23-3.322.20.1758120.9480.1320.2221.44797
3.32-3.422.30.1378210.9710.10.1721.33296.5
3.42-3.532.30.1257970.980.0920.1571.45495.1
3.53-3.652.20.1127840.9760.0840.1421.26995.3
3.65-3.82.20.0947330.9840.0660.1161.14887.4
3.8-3.972.30.0837830.9860.060.1041.03394.9
3.97-4.182.30.0718260.9880.0520.0891.0696.9
4.18-4.442.30.0658060.9890.0490.0821.09995.4
4.44-4.792.30.0567730.9920.0410.071.10793.6
4.79-5.272.30.057570.9950.0340.0621.17689.7
5.27-6.032.40.058190.9930.0360.0621.13997.7
6.03-7.592.30.0437690.9930.0340.0551.11991.8
7.59-502.40.03380210.0260.0431.13894.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 2.8→39.478 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.77
RfactorNum. reflection% reflection
Rfree0.2704 792 5.04 %
Rwork0.2311 --
obs0.2331 15728 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.12 Å2 / Biso mean: 62.1792 Å2 / Biso min: 33.14 Å2
Refinement stepCycle: final / Resolution: 2.8→39.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 57 0 2992
Biso mean--67.38 --
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053033
X-RAY DIFFRACTIONf_angle_d0.5434111
X-RAY DIFFRACTIONf_chiral_restr0.041460
X-RAY DIFFRACTIONf_plane_restr0.003518
X-RAY DIFFRACTIONf_dihedral_angle_d14.81757
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97540.32521320.3166251795
2.9754-3.2050.31221240.2731244793
3.205-3.52740.28581500.2553253796
3.5274-4.03740.25221350.2356245293
4.0374-5.08490.25051330.1999244593
5.0849-39.4780.26561180.2139253895
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)
11.03380.3254-1.70811.2728-2.07276.06860.1224-0.04890.10420.0021-0.2113-0.097-0.25870.34150.0190.44990.0026-0.09760.39840.03160.40553.5187-29.348-89.5884
22.0964-0.34590.42891.3096-0.08495.7861-0.3126-0.12050.19150.3766-0.0045-0.1495-0.76140.14940.02390.6228-0.085-0.10820.44820.01170.39673.7598-29.3277-52.5185
3-0.4499-0.4632-0.66621.1471-2.51165.69610.0887-0.140.13070.1084-0.2783-0.2483-0.49150.83280.18420.6181-0.1186-0.07320.61530.05570.49969.6011-31.1931-82.2385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 181 )A3 - 181
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 266 )A182 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 384 )A267 - 384

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