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- PDB-4nv6: C212A mutant of Synechococcus VKOR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4nv6
TitleC212A mutant of Synechococcus VKOR
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 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / Thioredoxin-like superfamily
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: 4.19 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers31,6531
Non-polymers8631
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)139.563, 139.563, 68.724
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: 31652.775 Da / Num. of mol.: 1 / Mutation: C212A
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.: 1 / 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 % sol: 79.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: A 20mg/ml protein solution was mixed overnight with 15mg/ml DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), and 0.5% DDM. This mixture was crystallized with a buffer containing 11% PEG1500, ...Details: A 20mg/ml protein solution was mixed overnight with 15mg/ml DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), and 0.5% DDM. This mixture was crystallized with a buffer containing 11% PEG1500, 8% glycerol, 5% ethanol, 0.1M MgCl2, 0.1M NaCl, and 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.19→50 Å / Num. all: 5743 / Num. obs: 5732 / % possible obs: 99.9 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.4
Reflection shellResolution: 4.19→4.27 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.3 / Num. unique all: 282 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PARROTphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.19→45.683 Å / SU ML: 0.53 / σ(F): 1.41 / Phase error: 41.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3311 571 9.99 %
Rwork0.2994 --
obs0.3022 5713 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.19→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 33 0 2027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052081
X-RAY DIFFRACTIONf_angle_d0.8422840
X-RAY DIFFRACTIONf_dihedral_angle_d14.459722
X-RAY DIFFRACTIONf_chiral_restr0.031327
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.19-4.61480.30291680.29481237X-RAY DIFFRACTION99
4.6148-5.28180.26191230.26221292X-RAY DIFFRACTION100
5.2818-6.65120.42451490.34741280X-RAY DIFFRACTION100
6.6512-45.68540.32811310.29641333X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.4539 Å / Origin y: -48.6099 Å / Origin z: 2.5404 Å
111213212223313233
T-1.0082 Å21.7547 Å2-0.449 Å2--0.7277 Å20.3404 Å2--0.1858 Å2
L0.2526 °20.1639 °2-0.0399 °2-0.1572 °2-0.036 °2--0.3179 °2
S0.089 Å °0.0232 Å °0.18 Å °-0.0257 Å °-0.4713 Å °0.0746 Å °0.9829 Å °0.4493 Å °-0.1654 Å °
Refinement TLS groupSelection details: ALL

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