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- PDB-5ien: Structure of CDL2.2, a computationally designed Vitamin-D3 binder -

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Basic information

Entry
Database: PDB / ID: 5ien
TitleStructure of CDL2.2, a computationally designed Vitamin-D3 binder
ComponentsCDL2.2
KeywordsDE NOVO PROTEIN / Rossetta / ligand binder / computational / Structural Genomics
Function / homologyNuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Chem-VDY
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.089 Å
AuthorsStoddard, B.L. / Doyle, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115545 United States
CitationJournal: Protein Eng.Des.Sel. / Year: 2018
Title: Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
Authors: Day, A.L. / Greisen, P. / Doyle, L. / Schena, A. / Stella, N. / Johnsson, K. / Baker, D. / Stoddard, B.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / struct
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: CDL2.2
B: CDL2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0175
Polymers30,1242
Non-polymers8933
Water1,49583
1
A: CDL2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5553
Polymers15,0621
Non-polymers4932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CDL2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4632
Polymers15,0621
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.831, 60.415, 93.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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Components

#1: Protein CDL2.2


Mass: 15061.948 Da / Num. of mol.: 2 / Fragment: computational design
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-VDY / 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL / 25-HYDROXYVITAMIN D3 / Calcifediol


Mass: 400.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES sodium pH 7.5, 1.4 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 16992 / % possible obs: 99.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 37.07 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.024 / Rrim(I) all: 0.082 / Χ2: 1.216 / Net I/av σ(I): 31.967 / Net I/σ(I): 13.5 / Num. measured all: 183753
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.167.80.53216190.9410.190.5660.97597.5
2.16-2.259.60.48316670.9620.1590.5091.01299.8
2.25-2.35110.41616740.970.1290.4361.0699.9
2.35-2.4811.50.37116630.9790.1130.3891.102100
2.48-2.6311.60.2516840.9890.0760.2621.128100
2.63-2.8411.70.17116850.9940.0520.1791.211100
2.84-3.1211.60.10817100.9970.0330.1131.316100
3.12-3.5711.60.0717070.9980.0210.0731.428100
3.57-4.511.30.04817430.9990.0150.051.386100
4.5-5010.40.04518400.9990.0150.0481.40299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.09 Å43.33 Å
Translation2.09 Å43.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HX8

3hx8


Resolution: 2.089→37.082 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1693 9.99 %
Rwork0.2058 15248 -
obs0.2093 16941 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.89 Å2 / Biso mean: 46.863 Å2 / Biso min: 27.72 Å2
Refinement stepCycle: final / Resolution: 2.089→37.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 160 83 2087
Biso mean--47.49 44.43 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031943
X-RAY DIFFRACTIONf_angle_d0.7622637
X-RAY DIFFRACTIONf_chiral_restr0.03291
X-RAY DIFFRACTIONf_plane_restr0.002331
X-RAY DIFFRACTIONf_dihedral_angle_d14.121678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1254X-RAY DIFFRACTION0.466TORSIONAL
12B1254X-RAY DIFFRACTION0.466TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.089-2.15040.30171270.26621143127091
2.1504-2.21980.30941400.23491271141199
2.2198-2.29920.27191370.23612361373100
2.2992-2.39120.31451390.234112531392100
2.3912-2.50.28111390.242812581397100
2.5-2.63180.27591410.215712631404100
2.6318-2.79660.2561430.235212811424100
2.7966-3.01250.28451410.243912761417100
3.0125-3.31550.26311420.215512741416100
3.3155-3.79480.23881450.197313001445100
3.7948-4.77940.19151440.162113071451100
4.7794-37.0880.20691550.19713861541100

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