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- PDB-6mog: Dimeric DARPin C_R3 -

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Basic information

Entry
Database: PDB / ID: 6mog
TitleDimeric DARPin C_R3
ComponentsDARPin C_R3
KeywordsBIOSYNTHETIC PROTEIN / DARPin
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsJude, K.M. / Mohan, K. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI51321 United States
CitationJournal: Science / Year: 2019
Title: Topological control of cytokine receptor signaling induces differential effects in hematopoiesis.
Authors: Mohan, K. / Ueda, G. / Kim, A.R. / Jude, K.M. / Fallas, J.A. / Guo, Y. / Hafer, M. / Miao, Y. / Saxton, R.A. / Piehler, J. / Sankaran, V.G. / Baker, D. / Garcia, K.C.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DARPin C_R3
B: DARPin C_R3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90113
Polymers35,1302
Non-polymers77111
Water3,243180
1
A: DARPin C_R3
hetero molecules

B: DARPin C_R3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90113
Polymers35,1302
Non-polymers77111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area3680 Å2
ΔGint3 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.250, 89.810, 44.270
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DARPin C_R3


Mass: 17565.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% PEG 3350, 1 mM reduced glutathione, 1 mM oxidized glutathione, 25% ethylene glycol cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.21→33.25 Å / Num. obs: 83274 / % possible obs: 88.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05076 / Rpim(I) all: 0.0208 / Net I/σ(I): 14.8
Reflection shellResolution: 1.21→1.253 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.564 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 8248 / CC1/2: 0.669 / Rpim(I) all: 0.6433 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSJun 1, 2017data reduction
XSCALEJun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 1.21→33.248 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.16
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1670 2.23 %random selection
Rwork0.1412 ---
obs0.1418 74923 88.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.21→33.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 50 180 2546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092497
X-RAY DIFFRACTIONf_angle_d1.0323399
X-RAY DIFFRACTIONf_dihedral_angle_d12.621919
X-RAY DIFFRACTIONf_chiral_restr0.079424
X-RAY DIFFRACTIONf_plane_restr0.007436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.24560.30431180.28164898X-RAY DIFFRACTION71
1.2456-1.28580.30681150.24415162X-RAY DIFFRACTION75
1.2858-1.33180.26381140.2215278X-RAY DIFFRACTION77
1.3318-1.38510.21881360.18555698X-RAY DIFFRACTION82
1.3851-1.44810.17371300.15135896X-RAY DIFFRACTION86
1.4481-1.52450.1691390.13296048X-RAY DIFFRACTION88
1.5245-1.620.19451480.11716444X-RAY DIFFRACTION93
1.62-1.74510.1741500.1156614X-RAY DIFFRACTION95
1.7451-1.92070.14091520.11096659X-RAY DIFFRACTION96
1.9207-2.19850.14341560.10556836X-RAY DIFFRACTION99
2.1985-2.76970.14171550.12516810X-RAY DIFFRACTION98
2.7697-33.26020.17861570.15666910X-RAY DIFFRACTION99

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