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- PDB-6bzx: Structure of the artificial complex alpha-Rep/Octarellin V.1 crys... -

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Basic information

Entry
Database: PDB / ID: 6bzx
TitleStructure of the artificial complex alpha-Rep/Octarellin V.1 crystallized by counter diffusion in a capillary
Components
  • Octarellin V.1
  • alpha-Rep
KeywordsDE NOVO PROTEIN / protein design / artificial protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.107 Å
AuthorsAedo, F. / Contreras-Martel, C. / Martinez-Oyanedel, J. / Bunster, M. / Minard, P. / Van de Weerdt, C. / Figueroa, M.
Funding support Chile, 1items
OrganizationGrant numberCountry
Universidad de ConcepcionVRID 217.037.023-1.OIN Chile
CitationJournal: To Be Published
Title: Crystallization of the artificial complex alpha-Rep/Octarellin V.1 by counter diffusion allowed to have a most complete structure
Authors: Aedo, F. / Figueroa, M.
History
DepositionDec 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-Rep
B: Octarellin V.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2533
Polymers57,2302
Non-polymers231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-21 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.562, 41.108, 81.409
Angle α, β, γ (deg.)90.00, 106.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha-Rep


Mass: 32362.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein Octarellin V.1


Mass: 24867.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 8 / Details: HEPES 0.1 M, MgCl 0.2 M, PEG 400 25%

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→45.14 Å / Num. obs: 8115 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 1 / Rrim(I) all: 0.108 / Net I/σ(I): 25.42
Reflection shellResolution: 3.1→3.29 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zv6

4zv6


Resolution: 3.107→38.941 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.81
RfactorNum. reflection% reflection
Rfree0.3036 862 10.65 %
Rwork0.2449 --
obs0.2511 8093 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.107→38.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 1 0 3716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023764
X-RAY DIFFRACTIONf_angle_d0.5235057
X-RAY DIFFRACTIONf_dihedral_angle_d16.3072319
X-RAY DIFFRACTIONf_chiral_restr0.039553
X-RAY DIFFRACTIONf_plane_restr0.004674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1071-3.30170.50671450.43281104X-RAY DIFFRACTION91
3.3017-3.55640.35661450.31821204X-RAY DIFFRACTION98
3.5564-3.9140.33321270.27141222X-RAY DIFFRACTION99
3.914-4.47970.30851570.23151217X-RAY DIFFRACTION99
4.4797-5.64120.30481530.25581221X-RAY DIFFRACTION99
5.6412-38.94380.24661350.1981263X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -0.2954 Å / Origin y: 0.4091 Å / Origin z: -20.9493 Å
111213212223313233
T0.8081 Å20.0085 Å20.1431 Å2-0.6803 Å2-0.0214 Å2--0.8917 Å2
L3.5865 °20.1792 °20.9631 °2-1.7096 °20.4616 °2--3.023 °2
S0.0325 Å °0.7757 Å °-0.0329 Å °-0.1878 Å °0.0277 Å °-0.0259 Å °0.1817 Å °0.0199 Å °-0.0247 Å °
Refinement TLS groupSelection details: all

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