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- PDB-4zfh: Crystal structure of Artificial ankyrin repeat protein_Ank(GAG)1D... -

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Basic information

Entry
Database: PDB / ID: 4zfh
TitleCrystal structure of Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -Y56A
ComponentsArtificial ankyrin repeat protein_Ank(GAG)1D4 mutant -Y56A
KeywordsPROTEIN BINDING / DARPins / Designed ankyrin repeat
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsChuankhayan, P. / Saoin, S. / Chupradit, K. / Wisitponchai, T. / Intachai, K. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. ...Chuankhayan, P. / Saoin, S. / Chupradit, K. / Wisitponchai, T. / Intachai, K. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J.
CitationJournal: To Be Published
Title: Crystal structure of Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant- Y56A
Authors: Chuankhayan, P. / Saoin, S. / Chupradit, K. / Wisitponchai, T. / Intachai, K. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -Y56A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2345
Polymers17,1371
Non-polymers974
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.839, 28.638, 53.537
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -Y56A


Mass: 17137.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 1000, reagent alcohol, sodium-phosphate dibasic/citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 11686 / % possible obs: 98 % / Redundancy: 5 % / Net I/σ(I): 6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.685 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27488 555 4.7 %RANDOM
Rwork0.2099 ---
obs0.21298 11131 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.11 Å2
2--0.1 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 4 110 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191205
X-RAY DIFFRACTIONr_bond_other_d0.0020.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9571633
X-RAY DIFFRACTIONr_angle_other_deg1.00532689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.47824.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29915200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.758159
X-RAY DIFFRACTIONr_chiral_restr0.1670.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
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_it1.8781.857623
X-RAY DIFFRACTIONr_mcbond_other1.8791.852622
X-RAY DIFFRACTIONr_mcangle_it2.9472.771777
X-RAY DIFFRACTIONr_mcangle_other2.9462.777778
X-RAY DIFFRACTIONr_scbond_it2.4112.197582
X-RAY DIFFRACTIONr_scbond_other2.412.197582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0143.149857
X-RAY DIFFRACTIONr_long_range_B_refined6.7216.1241405
X-RAY DIFFRACTIONr_long_range_B_other6.55715.6721369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 30 -
Rwork0.253 534 -
obs--61.64 %

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