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- PDB-4yy2: Computationally designed left-handed alpha/alpha toroid with 3 re... -

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Basic information

Entry
Database: PDB / ID: 4yy2
TitleComputationally designed left-handed alpha/alpha toroid with 3 repeats in space group P212121
ComponentsdTor_3x33L
KeywordsDE NOVO PROTEIN / Rosetta / toroid / alpha helix / computationally designed / left-handed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.854 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)R01 GM49857 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 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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
C: dTor_3x33L
D: dTor_3x33L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,85312
Polymers45,6694
Non-polymers1848
Water2,504139
1
A: dTor_3x33L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4633
Polymers11,4171
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: dTor_3x33L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5557
Polymers11,4171
Non-polymers1386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: dTor_3x33L


Theoretical massNumber of molelcules
Total (without water)11,4171
Polymers11,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: dTor_3x33L


Theoretical massNumber of molelcules
Total (without water)11,4171
Polymers11,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.139, 68.603, 152.357
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
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA2 - 1005 - 103
21GLYGLYLEULEUBB2 - 1005 - 103
12LYSLYSSERSERAA3 - 996 - 102
22LYSLYSSERSERCC3 - 996 - 102
13GLYGLYLEULEUAA2 - 1005 - 103
23GLYGLYLEULEUDD2 - 1005 - 103
14LYSLYSSERSERBB3 - 996 - 102
24LYSLYSSERSERCC3 - 996 - 102
15GLYGLYLEULEUBB2 - 1005 - 103
25GLYGLYLEULEUDD2 - 1005 - 103
16LYSLYSSERSERCC3 - 996 - 102
26LYSLYSSERSERDD3 - 996 - 102

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
dTor_3x33L


Mass: 11417.165 Da / Num. of mol.: 4 / Fragment: dTor_3x33L / Source method: obtained synthetically / Details: Rosetta designed / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3350, 0.2M Sodium Chloride, 100mM Tris pH 6.5

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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 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 30892 / % possible obs: 90.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.063 / Χ2: 1.1 / Net I/av σ(I): 20.275 / Net I/σ(I): 18.4 / Num. measured all: 186405
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.9270.531810.9510.2030.5410.90695.9
1.92-1.9970.34532020.9730.140.3731.06796.2
1.99-2.086.90.21332570.9880.0880.2311.16696.6
2.08-2.196.70.14432410.9920.060.1561.25696.5
2.19-2.336.30.10531980.9940.0460.1151.31495.3
2.33-2.515.90.08131320.9940.0370.091.22692.8
2.51-2.765.60.06729960.9950.0320.0751.20588.7
2.76-3.165.30.05528340.9960.0270.0621.09482.8
3.16-3.994.50.04726610.9960.0270.0550.87476.9
3.99-504.70.04331900.9970.0220.0490.70287

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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: Rosetta Design

Resolution: 1.854→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.941 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 1562 5.1 %RANDOM
Rwork0.2278 ---
obs0.2305 29249 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.52 Å2 / Biso mean: 42.074 Å2 / Biso min: 26.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.84 Å2
Refinement stepCycle: final / Resolution: 1.854→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 8 139 3185
Biso mean--61.51 52.95 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023070
X-RAY DIFFRACTIONr_bond_other_d0.0090.023104
X-RAY DIFFRACTIONr_angle_refined_deg1.7212.0274121
X-RAY DIFFRACTIONr_angle_other_deg1.62437253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59826.731104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90215643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.146157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023244
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02511
X-RAY DIFFRACTIONr_mcbond_it3.3333.6391576
X-RAY DIFFRACTIONr_mcbond_other3.3333.6371575
X-RAY DIFFRACTIONr_mcangle_it4.3615.431963
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A51990.19
12B51990.19
21A53800.18
22C53800.18
31A55250.17
32D55250.17
41B53320.17
42C53320.17
51B52990.18
52D52990.18
61C54900.18
62D54900.18
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 110 -
Rwork0.246 2208 -
all-2318 -
obs--94.19 %
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)
10.5483-0.0955-0.03420.4425-0.09950.3134-0.01180.0132-0.00050.01390.01560.01020.0285-0.037-0.00380.0114-0.00030.00170.02510.00360.01451.100275.16965.2199
20.6102-0.0622-0.00560.4404-0.06820.395-0.0388-0.0170.008-0.03140.0088-0.0107-0.0090.00440.030.02630.00220.00090.0016-0.0030.016917.497670.156125.6783
30.40970.0765-0.13190.84210.35920.88950.00320.0349-0.01770.0555-0.0152-0.02230.0662-0.00770.0120.01480.0012-0.01210.0142-0.00830.020313.336159.9681-12.7728
40.981-0.05810.15250.1841-0.10560.7183-0.00590.0778-0.0850.0216-0.019-0.02420.0369-0.00520.02490.0133-0.005-0.00340.0117-0.01330.0349-2.009793.815832.3657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 100
2X-RAY DIFFRACTION2B2 - 100
3X-RAY DIFFRACTION3C3 - 100
4X-RAY DIFFRACTION4D2 - 100

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