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- PDB-4nv5: C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated) -

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Basic information

Entry
Database: PDB / ID: 4nv5
TitleC50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated)
ComponentsVKORC1/thioredoxin domain protein
KeywordsOXIDOREDUCTASE / four helix bundle / thioredoxin-like protein / Membrane
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 / VKOR domain / 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 ...Vitamin K epoxide reductase-like VKOR/LOT1 / VKOR domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLiu, S. / Cheng, W. / Fowle Grider, R. / Shen, G. / Li, W.
CitationJournal: Nat Commun / Year: 2014
Title: Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.
Authors: Liu, S. / Cheng, W. / Fowle Grider, R. / Shen, G. / Li, W.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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
B: VKORC1/thioredoxin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers63,3062
Non-polymers1,7272
Water00
1
A: VKORC1/thioredoxin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers31,6531
Non-polymers8631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VKORC1/thioredoxin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers31,6531
Non-polymers8631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.842, 118.822, 68.034
Angle α, β, γ (deg.)90.00, 89.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.984315, -0.17457, -0.025462), (0.17449, -0.984644, 0.005363), (-0.026007, 0.000836, 0.999661)-71.13413, 35.26907, -35.06409

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Components

#1: Protein VKORC1/thioredoxin domain protein


Mass: 31652.775 Da / Num. of mol.: 2 / Mutation: C50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: JA-2-3B'a(2-13) / Gene: CYB_2278 / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2JJF6
#2: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
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: 4.5 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 12% PEG3350, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.664
11h,-k,-l20.336
ReflectionResolution: 2.79→50 Å / Num. all: 27621 / Num. obs: 27546 / % possible obs: 99.8 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.2
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PARROTphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→37.8 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.712 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24516 2733 9.9 %RANDOM
Rwork0.23228 ---
obs0.23355 24812 99.11 %-
all-24812 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.599 Å2
Baniso -1Baniso -2Baniso -3
1--49.48 Å2-0 Å23.25 Å2
2--18.91 Å20 Å2
3---30.57 Å2
Refinement stepCycle: LAST / Resolution: 2.79→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 66 0 3995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.91.9915616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0715515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.922.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44315595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8681519
X-RAY DIFFRACTIONr_chiral_restr0.0530.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213061
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 198 -
Rwork0.294 1678 -
obs--92.1 %
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)
15.05932.22-0.71262.0289-0.02410.5214-0.027-0.0584-0.19580.0141-0.008-0.05760.1529-0.11380.0350.4819-0.07260.03560.36430.03050.0138-22.462620.6596-19.3963
25.06433.2905-0.08864.1886-0.85340.92270.04430.08010.1240.23840.18390.305-0.24720.1572-0.22820.5274-0.00210.06440.4177-0.02090.0588-50.21616.686814.6427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 282
2X-RAY DIFFRACTION2B13 - 279

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