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- PDB-4ow4: Beta-trefoil designed by folding nucleus symmetric expansion ("Ph... -

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Basic information

Entry
Database: PDB / ID: 4ow4
TitleBeta-trefoil designed by folding nucleus symmetric expansion ("Phifoil")
ComponentsBeta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")
KeywordsDE NOVO PROTEIN / Beta-trefoil / folding nucleus symmetric expansion / protein design / de novo / top-down symmetric deconstruction
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsBlaber, M. / Longo, L.M.
CitationJournal: Structure / Year: 2014
Title: Evolution and design of protein structure by folding nucleus symmetric expansion.
Authors: Longo, L.M. / Kumru, O.S. / Middaugh, C.R. / Blaber, M.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords / struct_ncs_dom_lim / struct_site
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")
B: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6483
Polymers27,5522
Non-polymers961
Water2,378132
1
A: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")


Theoretical massNumber of molelcules
Total (without water)13,7761
Polymers13,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8722
Polymers13,7761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")

B: Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6483
Polymers27,5522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_845-x+3,y-1/2,-z+1/21
Buried area1740 Å2
ΔGint-19 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.861, 68.634, 76.044
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
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 10 - 136 / Label seq-ID: 1 - 123

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

NCS ensembles :
ID
1
2

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Components

#1: Protein Beta-terfoil designed by folding nucleus symmetric expansion ("Phifoil")


Mass: 13776.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 800 mM Ammonium Sulfate, 100 mM Citric Acid, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 27, 2013
RadiationMonochromator: Multi-layer mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 12829 / % possible obs: 81.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Χ2: 3.995 / Net I/av σ(I): 18.816 / Net I/σ(I): 12.6 / Num. measured all: 27752
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.2120.19611190.96286.9
2.21-2.282.10.16210711.14784.3
2.28-2.3720.14710951.2685.3
2.37-2.462.10.1510991.42785.4
2.46-2.572.20.14311011.68786.1
2.57-2.712.10.11810831.78484
2.71-2.882.10.110782.3483
2.88-3.12.20.08710863.8983
3.1-3.412.20.07210434.74980.2
3.41-3.912.10.06410215.52777.8
3.91-4.922.30.06710129.66975.1
4.92-402.40.064102111.67371.5

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1606)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.148→28.151 Å / FOM work R set: 0.7708 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 640 5 %
Rwork0.2293 12169 -
obs0.2312 12809 81.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.52 Å2 / Biso mean: 27.76 Å2 / Biso min: 10.92 Å2
Refinement stepCycle: final / Resolution: 2.148→28.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 5 132 2073
Biso mean--49.29 33.71 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051968
X-RAY DIFFRACTIONf_angle_d0.9372667
X-RAY DIFFRACTIONf_chiral_restr0.045307
X-RAY DIFFRACTIONf_plane_restr0.004353
X-RAY DIFFRACTIONf_dihedral_angle_d11.056745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1116X-RAY DIFFRACTION3.957TORSIONAL
12B1116X-RAY DIFFRACTION3.957TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1475-2.31330.28441310.23532496262785
2.3133-2.54590.31831310.24742492262385
2.5459-2.9140.30391300.26242476260684
2.914-3.67010.27321260.23352394252080
3.6701-28.15320.22481220.20152311243374

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