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- PDB-5c2m: The de novo evolutionary emergence of a symmetrical protein is sh... -

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Basic information

Entry
Database: PDB / ID: 5c2m
TitleThe de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
ComponentsPredicted protein
KeywordsSTRUCTURAL PROTEIN / beta-propeller
Function / homologyTachylectin 2 / Tachylectin 2 / Tachylectin 2 superfamily / Tachylectin / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta / Tachylectin 2 domain-containing protein
Function and homology information
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Predicted protein


Theoretical massNumber of molelcules
Total (without water)28,1801
Polymers28,1801
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.693, 60.929, 88.351
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 Predicted protein


Mass: 28179.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematostella vectensis (starlet sea anemone)
Gene: v1g114158 / Production host: Escherichia coli (E. coli) / References: UniProt: A7SDD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1M NaF, 0.05 M Bis-Tris propane pH 7.5, 10% polyethylene glycol 3,350.

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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: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19656 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.042 / Net I/σ(I): 29.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TL2

1tl2


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.783 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23485 1002 5.1 %RANDOM
Rwork0.19068 ---
obs0.1929 18599 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.718 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0.5 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 81 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.922656
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0445237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3023.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5115277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.608155
X-RAY DIFFRACTIONr_chiral_restr0.1580.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211549
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_other35.9
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_it1.6371.51175
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56721868
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7273779
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1324.5788
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.38931954
X-RAY DIFFRACTIONr_sphericity_free9.711382
X-RAY DIFFRACTIONr_sphericity_bonded4.6431879
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 62 -
Rwork0.281 1329 -
obs--97.68 %

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