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- PDB-5et3: Crystal Structure of De novo Designed Fullerene organizing peptide -

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Basic information

Entry
Database: PDB / ID: 5et3
TitleCrystal Structure of De novo Designed Fullerene organizing peptide
ComponentsFullerene Organizing Protein (C60Sol-COP-3)
KeywordsDE NOVO PROTEIN / fullerene / complex / helical assembly
Function / homology(C_{60}-I_{h})[5,6]fullerene
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.671 Å
AuthorsKim, K.-H. / Kim, Y.H. / Acharya, R. / Kim, N.H. / Paul, J. / Grigoryan, G. / DeGrado, W.F.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2014R1A1A2055647 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2016
Title: Protein-directed self-assembly of a fullerene crystal.
Authors: Kim, K.-H. / Ko, D.-K. / Kim, Y.-T. / Kim, N.H. / Paul, J. / Zhang, S.-Q. / Murray, C.B. / Acharya, R. / DeGrado, W.F. / Kim, Y.H. / Grigoryan, G.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Fullerene Organizing Protein (C60Sol-COP-3)
B: Fullerene Organizing Protein (C60Sol-COP-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0983
Polymers6,3772
Non-polymers7211
Water52229
1
A: Fullerene Organizing Protein (C60Sol-COP-3)
B: Fullerene Organizing Protein (C60Sol-COP-3)
hetero molecules

A: Fullerene Organizing Protein (C60Sol-COP-3)
B: Fullerene Organizing Protein (C60Sol-COP-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1966
Polymers12,7544
Non-polymers1,4412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area5380 Å2
ΔGint-51 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.145, 42.145, 66.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein/peptide Fullerene Organizing Protein (C60Sol-COP-3)


Mass: 3188.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-60C / (C_{60}-I_{h})[5,6]fullerene / buckminsterfullerene, buckyball


Mass: 720.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: The 2 uL drop consisted of a 1:1 v/v mixture of 8 mg/ml complex solution in 25 mM Tris pH 8.0 and reservoir solution consisting of 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic ...Details: The 2 uL drop consisted of a 1:1 v/v mixture of 8 mg/ml complex solution in 25 mM Tris pH 8.0 and reservoir solution consisting of 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2014
Diffraction measurementDetails: 1.00 degrees, 1.0 sec, detector distance 200.00 mm / Method: \w scans
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.066 / Number: 122822
ReflectionResolution: 1.67→50 Å / Num. obs: 7537 / % possible obs: 95.9 % / Redundancy: 16.3 % / Biso Wilson estimate: 11.04 Å2 / Rmerge(I) obs: 0.066 / Χ2: 0.947 / Net I/av σ(I): 30.99 / Net I/σ(I): 17.5 / Num. measured all: 122822
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.67-1.7311.30.1887851.0899.7
1.73-1.813.70.1477701.037100
1.8-1.8814.70.1327771.117100
1.88-1.98160.1127861.12100
1.98-2.117.10.0977961.09599.9
2.1-2.2718.20.0837711.06199.9
2.27-2.4918.70.0747850.92899.9
2.49-2.8618.90.0637690.7998.8
2.86-3.618.70.0557460.65993.5
3.6-5015.60.0525520.57568.2
Cell measurementReflection used: 122822

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2306: ???refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S0R

3s0r


Resolution: 1.671→15.304 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 752 10.04 %
Rwork0.2181 6735 -
obs0.2207 7487 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.13 Å2 / Biso mean: 22.5022 Å2 / Biso min: 9.15 Å2
Refinement stepCycle: final / Resolution: 1.671→15.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 60 29 535
Biso mean--27.46 30.48 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008536
X-RAY DIFFRACTIONf_angle_d0.893778
X-RAY DIFFRACTIONf_chiral_restr0.03370
X-RAY DIFFRACTIONf_plane_restr0.22281
X-RAY DIFFRACTIONf_dihedral_angle_d21.212166
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 (%)
1.6715-1.80030.25211540.21411372152698
1.8003-1.98120.24751580.20614031561100
1.9812-2.26710.21321550.194714001555100
2.2671-2.85320.22281500.19851399154999
2.8532-15.30450.27641350.2571161129681
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)
11.8346-0.1721.05122.5477-1.64055.49790.12840.05490.24510.0067-0.0784-0.1052-0.2886-0.22350.2840.08370.03550.03190.1210.06840.11414.42140.8734.323
22.07860.04971.10352.68511.71975.52690.1036-0.03540.1369-0.0869-0.09890.0519-0.35860.19260.27430.083-0.0270.03040.1131-0.04550.1202-4.424240.88296.3203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A1 - 30
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 30 )B1 - 30

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