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- PDB-3kp9: Structure of a bacterial homolog of vitamin K epoxide reductase -

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Basic information

Entry
Database: PDB / ID: 3kp9
TitleStructure of a bacterial homolog of vitamin K epoxide reductase
ComponentsVKORC1/thioredoxin domain protein
KeywordsBlood Coagulation / OXIDOREDUCTASE / Warfarin / Disulfide formation
Function / homology
Function and homology information


Oxidoreductases; Acting on CH or CH2 groups; With a disulfide as acceptor / quinone binding / oxidoreductase activity / membrane
Similarity search - Function
VKOR domain / Vitamin K epoxide reductase-like VKOR/LOT1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...VKOR domain / Vitamin K epoxide reductase-like VKOR/LOT1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / UBIQUINONE-10 / Vitamin K epoxide reductase homolog
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.6 Å
AuthorsLi, W. / Schulman, S. / Dutton, R.J. / Boyd, D. / Beckwith, J. / Rapoport, T.A.
CitationJournal: Nature / Year: 2010
Title: Structure of a bacterial homologue of vitamin K epoxide reductase.
Authors: Li, W. / Schulman, S. / Dutton, R.J. / Boyd, D. / Beckwith, J. / Rapoport, T.A.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VKORC1/thioredoxin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9334
Polymers31,6691
Non-polymers1,2653
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.942, 136.942, 68.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein VKORC1/thioredoxin domain protein


Mass: 31668.775 Da / Num. of mol.: 1 / Mutation: C56S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: JA-2-3B'a(2-13) / Gene: CYB_2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2JJF6, EC: 1.1.4.2
#2: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg

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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: 5.85 Å3/Da / Density % sol: 78.985 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 15% PEG1000, 0.2M magnesium chloride, pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.00718 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: MIR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00718 Å / Relative weight: 1
ReflectionResolution: 3.6→118.6 Å / Num. all: 8650 / Num. obs: 8572 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 3.6→44.83 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.855 / SU B: 44.419 / SU ML: 0.333 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.581 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Judging from the experimental electron density map, there is density between Cys130 and Cys133, indicative of a disulfide bridge, as well ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Judging from the experimental electron density map, there is density between Cys130 and Cys133, indicative of a disulfide bridge, as well as density suggesting a covalent bond between the quinone ring of U10 and Cys133. We have not been able to use a refinement program to optimize both bond lengths at the same time
RfactorNum. reflection% reflectionSelection details
Rfree0.305 855 10 %RANDOM
Rwork0.25114 ---
obs0.25627 7714 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.017 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å21.37 Å20 Å2
2--2.74 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 3.6→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 35 0 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9892805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.795256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57722.20668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.00115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5641510
X-RAY DIFFRACTIONr_chiral_restr0.1060.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211519
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3551.51283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69222056
X-RAY DIFFRACTIONr_scbond_it0.8473768
X-RAY DIFFRACTIONr_scangle_it1.4434.5749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 67 -
Rwork0.293 558 -
obs--96.75 %
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)
146.0780.5225-0.461715.284121.03668.22020.0983-2.9582.33450.4986-0.77310.2998-0.7482-1.05850.67482.2956-1.38210.5422.0420.52231.083118.984850.923112.4686
2-1.7365-1.8275-1.00540.72482.462712.23790.35860.12780.2419-0.01830.6247-0.62762.11931.0228-0.98330.8842-0.3225-0.21231.4523-0.46030.75440.875460.60229.7477
311.96426.7598-2.2411.6312-0.16472.5931-0.50281.2689-0.6467-0.65850.4053-0.4276-0.7538-0.29620.09751.46770.11810.12131.016-0.04261.51850.976773.648316.0345
47.43442.439-1.23282.00721.031410.60690.12150.2352-0.49320.23650.09340.09451.2643-1.3395-0.21490.5766-0.6024-0.1120.8080.10320.81832.80158.632722.6571
511.3343.07553.8065.34620.25146.076-0.0515-0.64140.38960.33440.1206-0.0264-0.3433-0.28-0.06910.4952-0.0531-0.0880.4649-0.02981.182358.670386.086323.6554
623.6889-10.98283.90824.43771.591916.4774-1.6816-0.26541.41880.71640.0549-0.33310.9752-0.6751.62670.6581-0.2099-0.27520.6086-0.01661.49573.364985.094829.9074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 20
2X-RAY DIFFRACTION2A21 - 44
3X-RAY DIFFRACTION3A45 - 70
4X-RAY DIFFRACTION4A71 - 177
5X-RAY DIFFRACTION5A178 - 272
6X-RAY DIFFRACTION6A273 - 279

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