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- PDB-4ydw: CRYSTAL STRUCTURE OF ANTI-IL4 DARPIN 44C12V5 -

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Basic information

Entry
Database: PDB / ID: 4ydw
TitleCRYSTAL STRUCTURE OF ANTI-IL4 DARPIN 44C12V5
ComponentsDARPIN 44C12V5
KeywordsDE NOVO PROTEIN / ALTERNATIVE SCAFFOLD
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF ANTI-IL4 DARPIN 44C12V5
Authors: Teplyakov, A. / Obmolova, G. / Gilliland, G.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DARPIN 44C12V5
B: DARPIN 44C12V5


Theoretical massNumber of molelcules
Total (without water)35,7742
Polymers35,7742
Non-polymers00
Water3,063170
1
A: DARPIN 44C12V5


Theoretical massNumber of molelcules
Total (without water)17,8871
Polymers17,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DARPIN 44C12V5


Theoretical massNumber of molelcules
Total (without water)17,8871
Polymers17,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.240, 60.740, 81.890
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 DARPIN 44C12V5


Mass: 17887.037 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 23% PEG 3350, 0.2 M DI-AMMONIUM CITRATE, 3% DIOXANE, 3% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 11, 2014 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 22846 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 43.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 7.8 / % possible all: 71.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDY

4ydy


Resolution: 1.9→25.744 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.907 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.21229 1168 5.1 %RANDOM
Rwork0.17002 ---
obs0.17206 21630 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å20 Å2
2---0.9 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 170 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9683190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6615311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45426.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.264156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211774
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.312.0591250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1874.5511559
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.6992.8641093
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.9463660
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 63 -
Rwork0.186 1173 -
obs--71.69 %

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