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- PDB-4yy5: Computationally designed left-handed alpha/alpha toroid with 3 re... -

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Basic information

Entry
Database: PDB / ID: 4yy5
TitleComputationally designed left-handed alpha/alpha toroid with 3 repeats in space group P43212
ComponentsdTor_3x33L
KeywordsDE NOVO PROTEIN / Rosetta / toroid / alpha helix / computationally designed / left-handed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsHallinan, J.P. / Bradley, P. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nature / Year: 2015
Title: Rational design of alpha-helical tandem repeat proteins with closed architectures.
Authors: Doyle, L. / Hallinan, J. / Bolduc, J. / Parmeggiani, F. / Baker, D. / Stoddard, B.L. / Bradley, P.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTor_3x33L
B: dTor_3x33L


Theoretical massNumber of molelcules
Total (without water)22,1102
Polymers22,1102
Non-polymers00
Water90150
1
A: dTor_3x33L


Theoretical massNumber of molelcules
Total (without water)11,0551
Polymers11,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dTor_3x33L


Theoretical massNumber of molelcules
Total (without water)11,0551
Polymers11,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.184, 40.184, 217.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 98 / Label seq-ID: 2 - 97

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein dTor_3x33L


Mass: 11054.763 Da / Num. of mol.: 2 / Fragment: dTor_3x33L / Source method: obtained synthetically / Details: Rosetta designed / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 45% PEG 400

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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 SATURN 944+ / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 5071 / % possible obs: 98.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.013 / Rrim(I) all: 0.05 / Χ2: 1.184 / Net I/av σ(I): 26.962 / Net I/σ(I): 28 / Num. measured all: 62120
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.78-2.8810.60.1364990.9950.0410.1421.20598.2
2.88-2.99140.1124690.9970.0290.1161.14599.8
2.99-3.1313.30.094950.9970.0240.0941.149100
3.13-3.312.70.0774860.9980.0210.081.15799.2
3.3-3.512.20.064890.9980.0170.0631.10399.8
3.5-3.77110.0534950.9990.0150.0551.08998.2
3.77-4.1510.40.0464970.9980.0150.0491.43497.8
4.15-4.759.40.0385160.9990.0130.041.14499.4
4.75-5.9911.20.0425290.9990.0130.0441.133100
5.99-50170.0395960.9990.0090.0411.25897.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally designed model

Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.896 / SU B: 36.009 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 261 5.2 %RANDOM
Rwork0.1974 ---
obs0.2012 4760 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.26 Å2 / Biso mean: 35.873 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 2.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 0 50 1530
Biso mean---60.36 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021496
X-RAY DIFFRACTIONr_bond_other_d0.0010.021496
X-RAY DIFFRACTIONr_angle_refined_deg1.9212.0222014
X-RAY DIFFRACTIONr_angle_other_deg2.85433481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8226.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97115298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.628154
X-RAY DIFFRACTIONr_chiral_restr0.0780.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021596
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02256
X-RAY DIFFRACTIONr_mcbond_it2.1332.76782
X-RAY DIFFRACTIONr_mcbond_other2.132.758781
X-RAY DIFFRACTIONr_mcangle_it3.4284.133974
Refine LS restraints NCS

Ens-ID: 1 / Number: 5012 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.779→2.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 19 -
Rwork0.239 351 -
all-370 -
obs--95.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3607-0.1674-0.37732.29680.44152.09360.0211-0.0795-0.11640.0609-0.08680.0427-0.0348-0.13370.06560.0575-0.0032-0.04020.01960.00490.0389.5511-4.3638-14.0407
21.94760.53590.01731.2481-0.54682.32360.0068-0.1138-0.0211-0.0802-0.0709-0.16940.04660.10870.06410.01140.00280.00670.0230.00760.030228.572513.5307-14.0509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 99
2X-RAY DIFFRACTION2B2 - 100

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