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- PDB-5hkr: Crystal structure of de novo designed fullerene organising protei... -

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Basic information

Entry
Database: PDB / ID: 5hkr
TitleCrystal structure of de novo designed fullerene organising protein complex with fullerene
Componentsfullerene organizing protein
KeywordsDE NOVO PROTEIN / Fullerene protein complex / De novo protein design
Function / homology(C_{60}-I_{h})[5,6]fullerene
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsAcharya, R. / Kim, Y.H. / Grigoryan, G. / DeGardo, W.F.
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
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: fullerene organizing protein
B: fullerene organizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0983
Polymers6,3772
Non-polymers7211
Water1086
1
A: fullerene organizing protein
B: fullerene organizing protein
hetero molecules

A: fullerene organizing protein
B: fullerene organizing protein
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_455-x-1,-y,z1
Buried area5430 Å2
ΔGint-46 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.713, 41.713, 66.808
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein/peptide fullerene organizing protein


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.: 6 / 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: 2.37 Å3/Da / Density % sol: 53.25 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM sodium phosphate, 100mM NaCl pH 7.5, 17mM lithium sulfate monohydrate, 85mM tris-hcl sodium pH 8.5, 25.5% PEG 4000, 25%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 5598 / % possible obs: 100 % / Redundancy: 13.7 % / Rsym value: 0.135 / Net I/σ(I): 15.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.35→36.125 Å / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 24.16 / Stereochemistry target values: TWIN_LSQ_F
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2338 511 9.43 %
Rwork0.2019 --
obs0.2092 5421 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→36.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 60 6 512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007536
X-RAY DIFFRACTIONf_angle_d0.808778
X-RAY DIFFRACTIONf_dihedral_angle_d24.996286
X-RAY DIFFRACTIONf_chiral_restr0.0370
X-RAY DIFFRACTIONf_plane_restr0.00380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3649-2.60160.25421210.22741221X-RAY DIFFRACTION91
2.6016-2.97490.24461320.22081193X-RAY DIFFRACTION90
2.9749-3.73630.26611280.20551190X-RAY DIFFRACTION90
3.7363-14.02830.20541300.19291195X-RAY DIFFRACTION90

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