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- PDB-3kp8: The thioredoxin-like domain of a VKOR homolog from Synechococcus sp. -

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Basic information

Entry
Database: PDB / ID: 3kp8
TitleThe thioredoxin-like domain of a VKOR homolog from Synechococcus sp.
ComponentsVKORC1/thioredoxin domain protein
KeywordsOXIDOREDUCTASE / Blood Coagulation / Disulfide formation / Redox partner
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
Vitamin K epoxide reductase-like VKOR/LOT1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Vitamin K epoxide reductase homolog
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 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 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VKORC1/thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)11,5711
Polymers11,5711
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.088, 57.088, 57.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-19-

HOH

21A-50-

HOH

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Components

#1: Protein VKORC1/thioredoxin domain protein


Mass: 11570.846 Da / Num. of mol.: 1 / Fragment: residues 186-283
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.8
Details: 0.6M sodium potassium tartrate, 10% PEG MME 5000, pH 7.8, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 11831 / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.66→33.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.862 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.136 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21214 565 4.8 %RANDOM
Rwork0.19441 ---
obs0.19527 11208 99.87 %-
all-11819 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.66→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 0 53 757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.952995
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.943593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6842430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9421597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.85153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022573
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_it0.7671.5466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3892745
X-RAY DIFFRACTIONr_scbond_it1.9093260
X-RAY DIFFRACTIONr_scangle_it2.9974.5250
X-RAY DIFFRACTIONr_rigid_bond_restr1.0713726
X-RAY DIFFRACTIONr_sphericity_free3.72353
X-RAY DIFFRACTIONr_sphericity_bonded2.2523704
LS refinement shellResolution: 1.66→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 42 -
Rwork0.243 807 -
obs--100 %

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