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- PDB-5aq8: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -

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Basic information

Entry
Database: PDB / ID: 5aq8
TitleDARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
ComponentsOFF7_DB12V4
KeywordsCHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION
Function / homologyAnkyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / THIOCYANATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsBatyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: OFF7_DB12V4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6146
Polymers45,9631
Non-polymers6515
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 76.640, 106.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OFF7_DB12V4


Mass: 45962.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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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: 1.75 Å3/Da / Density % sol: 29.7 % / Description: NONE
Crystal growpH: 7.5
Details: PEG4000 18.3 %, KSCN 0.286 M, HEPES-NA, 0.1 M, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→43.72 Å / Num. obs: 43423 / % possible obs: 1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.13
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.51 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A

3dtm

1svx


Resolution: 1.62→43.717 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2172 5 %
Rwork0.1862 --
obs0.1887 43419 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.04 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 39 289 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023228
X-RAY DIFFRACTIONf_angle_d0.6584377
X-RAY DIFFRACTIONf_dihedral_angle_d11.2981199
X-RAY DIFFRACTIONf_chiral_restr0.037502
X-RAY DIFFRACTIONf_plane_restr0.003567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6199-1.65510.31911330.26082526X-RAY DIFFRACTION99
1.6551-1.69360.43911340.26552528X-RAY DIFFRACTION100
1.6936-1.7360.34691330.25622529X-RAY DIFFRACTION99
1.736-1.78290.30361360.26682583X-RAY DIFFRACTION99
1.7829-1.83540.2911320.25092512X-RAY DIFFRACTION100
1.8354-1.89460.35011330.24512532X-RAY DIFFRACTION99
1.8946-1.96230.2691360.22512573X-RAY DIFFRACTION99
1.9623-2.04090.26071340.20042546X-RAY DIFFRACTION100
2.0409-2.13380.23661340.16912552X-RAY DIFFRACTION100
2.1338-2.24630.24441350.15882567X-RAY DIFFRACTION100
2.2463-2.3870.21511360.16732585X-RAY DIFFRACTION100
2.387-2.57130.22821370.17412592X-RAY DIFFRACTION100
2.5713-2.830.23931360.17412589X-RAY DIFFRACTION100
2.83-3.23940.23511380.18452624X-RAY DIFFRACTION100
3.2394-4.08090.17041390.16362646X-RAY DIFFRACTION99
4.0809-43.73260.20911460.17482763X-RAY DIFFRACTION99

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