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- PDB-5c2n: The de novo evolutionary emergence of a symmetrical protein is sh... -

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Basic information

Entry
Database: PDB / ID: 5c2n
TitleThe de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
ComponentsBeta propeller
KeywordsUNKNOWN FUNCTION / bladed beta propeller
Function / homologyTachylectin 2 / Tachylectin 2 superfamily / Tachylectin / Beta propeller
Function and homology information
Biological speciesEnterobacteria phage L1 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsSmock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S.
CitationJournal: Cell / Year: 2016
Title: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.
Authors: Smock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Beta propeller
B: Beta propeller
C: Beta propeller
D: Beta propeller
E: Beta propeller
F: Beta propeller
G: Beta propeller
H: Beta propeller
I: Beta propeller
J: Beta propeller
K: Beta propeller
L: Beta propeller
M: Beta propeller
N: Beta propeller
O: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,01230
Polymers79,69415
Non-polymers3,31815
Water9,008500
1
B: Beta propeller
D: Beta propeller
F: Beta propeller
H: Beta propeller
J: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,67110
Polymers26,5655
Non-polymers1,1065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta propeller
C: Beta propeller
E: Beta propeller
G: Beta propeller
I: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,67110
Polymers26,5655
Non-polymers1,1065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
K: Beta propeller
L: Beta propeller
M: Beta propeller
N: Beta propeller
O: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,67110
Polymers26,5655
Non-polymers1,1065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.219, 112.219, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11O-215-

HOH

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Components

#1: Protein/peptide
Beta propeller


Mass: 5312.904 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage L1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140UHM9*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.05 M PCB buffer (2:1:2 ratio of sodium propionate, sodium cacodylate and Bis-Tris propane, pH 7) 12% polyethylene glycol 1,500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 92166 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.65→30.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.318 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24753 4637 5 %RANDOM
Rwork0.18613 ---
obs0.1893 87992 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.546 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.55 Å2-0 Å2
2---0.55 Å2-0 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 75 500 6211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025926
X-RAY DIFFRACTIONr_bond_other_d0.0030.025207
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9628070
X-RAY DIFFRACTIONr_angle_other_deg1.2233.02212027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.83623.866269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47415776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0091515
X-RAY DIFFRACTIONr_chiral_restr0.1970.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021496
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.818311133
X-RAY DIFFRACTIONr_sphericity_free18.525144
X-RAY DIFFRACTIONr_sphericity_bonded9.089511296
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 306 -
Rwork0.313 6505 -
obs--100 %

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