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Basic information

Entry
Database: PDB / ID: 6wvi
TitleVKOR-like from Takifugu rubripes
ComponentsVitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
KeywordsMEMBRANE PROTEIN / Vitamin K epoxide Reductase / VKOR / VKOR-like protein / VKORL / Vitamin K / warfarin / superwarfarin / vitamin K expoxide / KO
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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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: 2.4 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 6, 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 / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_mod_residue.parent_comp_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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

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)47,1392
Polymers46,7831
Non-polymers3571
Water86548
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 area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.639, 49.064, 84.326
Angle α, β, γ (deg.)90.000, 112.730, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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)
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.14 %
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 PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 22666 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 48.24 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.067 / Rrim(I) all: 0.136 / Χ2: 1.062 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.81.39211540.3480.8041.6161.11499.5
2.44-2.493.81.23911180.4370.7221.4421.03199.3
2.49-2.533.81.15811050.3990.6821.3511.08698.4
2.53-2.593.61.00811410.5130.61.1811.08798.4
2.59-2.644.20.94211100.5590.521.0821.06699.5
2.64-2.74.20.75211290.6590.4140.8631.09299.6
2.7-2.774.20.58111210.7640.3240.6681.09199.4
2.77-2.854.20.52711190.8140.2920.6051.11999.7
2.85-2.934.20.48411480.830.2680.5561.13699.3
2.93-3.024.10.33411360.9030.1890.3861.02899.5
3.02-3.133.80.25311000.9430.1490.2951.06497.5
3.13-3.264.10.20311360.9530.1150.2351.05599.2
3.26-3.414.30.15411300.9670.0860.1771.05299.7
3.41-3.584.30.12111390.980.0670.1391.02499.7
3.58-3.814.10.09811480.9850.0550.1131.0799.5
3.81-4.13.80.08111290.9910.0470.0941.05898
4.1-4.5240.06111290.9940.0330.071.01498.9
4.52-5.174.20.05211470.9960.0280.0591.00599
5.17-6.513.80.04711490.9970.0260.0540.9998.4
6.51-503.90.0411780.9970.0230.0461.06596.6

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Processing

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

2b3p


Resolution: 2.4→35.43 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1090 4.82 %
Rwork0.1968 21542 -
obs0.1986 22632 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.34 Å2 / Biso mean: 68.5945 Å2 / Biso min: 27.16 Å2
Refinement stepCycle: final / Resolution: 2.4→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 17 48 3321
Biso mean--85.92 67.37 -
Num. residues----412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.510.28321300.24912498262892
2.51-2.640.26491350.24132690282598
2.64-2.80.29171510.2192678282999
2.8-3.020.26741360.221227112847100
3.02-3.320.22581250.19512715284099
3.32-3.80.23671430.197527472890100
3.8-4.790.21541400.17832708284898
4.79-35.430.2171300.18662795292598
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)
17.2135-0.26141.3483.4131-0.31614.9026-0.12160.2953-0.1868-0.17260.2216-0.1051-0.15380.0902-0.05720.2201-0.01090.02540.26160.01750.258120.629-21.62740.8201
24.4897-0.4786-0.52542.2105-0.88926.184-0.0158-0.0882-0.37310.0525-0.14050.08580.5435-0.96220.17310.6866-0.07170.02090.5927-0.01990.38942.9358-18.820843.4084
34.34272.55-0.31972.44760.53971.05-0.2659-0.01230.4416-0.0345-0.01770.0242-0.0543-0.2040.20320.45530.0651-0.0590.51610.01810.300515.5512-14.978511.7015
46.47910.71850.95593.7698-0.19043.7722-0.1145-0.74050.06230.38680.13520.0034-0.3794-0.35760.01860.29890.06490.02810.29880.01880.261818.5035-16.9299.3989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 150 )A2 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 303 )A151 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 328 )A304 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 415 )A329 - 415

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