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- PDB-5dn0: t1555 loop variant -

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Basic information

Entry
Database: PDB / ID: 5dn0
Titlet1555 loop variant
Componentsbeta1 t1555 loop variant
KeywordsDE NOVO PROTEIN / synthetic protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsMacDonald, J.T. / Kabasakal, B.V. / Murray, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: beta1 t1555 loop variant


Theoretical massNumber of molelcules
Total (without water)25,6331
Polymers25,6331
Non-polymers00
Water00
1
A: beta1 t1555 loop variant

A: beta1 t1555 loop variant


Theoretical massNumber of molelcules
Total (without water)51,2662
Polymers51,2662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.270, 108.270, 151.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein beta1 t1555 loop variant


Mass: 25633.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: 30% v/v glycerol pH7, 1.26M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 4.4→88.01 Å / Num. all: 25067 / Num. obs: 3058 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.088 / Net I/av σ(I): 10.65 / Net I/σ(I): 14.3
Reflection shellResolution: 4.4→4.51 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.4→88.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.874 / SU B: 63.285 / SU ML: 0.741 / Cross valid method: THROUGHOUT / ESU R Free: 1.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33089 150 4.9 %RANDOM
Rwork0.25404 ---
obs0.25728 2899 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 204.917 Å2
Baniso -1Baniso -2Baniso -3
1-5.68 Å2-0 Å20 Å2
2--5.68 Å2-0 Å2
3----11.36 Å2
Refinement stepCycle: 1 / Resolution: 4.4→88.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 0 0 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191630
X-RAY DIFFRACTIONr_bond_other_d0.0020.021552
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9472215
X-RAY DIFFRACTIONr_angle_other_deg1.06133521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7845220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59625.59584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.571512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021993
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
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_it16.81419.71883
X-RAY DIFFRACTIONr_mcbond_other16.77219.71882
X-RAY DIFFRACTIONr_mcangle_it26.15529.5981102
X-RAY DIFFRACTIONr_mcangle_other26.14529.61103
X-RAY DIFFRACTIONr_scbond_it16.13321.493746
X-RAY DIFFRACTIONr_scbond_other16.11521.487746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other26.30631.6371113
X-RAY DIFFRACTIONr_long_range_B_refined37.4987059
X-RAY DIFFRACTIONr_long_range_B_other37.4957060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.4→4.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 12 -
Rwork0.2 213 -
obs--99.12 %

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