[English] 日本語
Yorodumi
- PDB-6wvb: Takifugu rubripes VKOR-like with warfarin -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more