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- PDB-5hkn: Crystal structure de novo designed fullerene organizing protein c... -

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Basic information

Entry
Database: PDB / ID: 5hkn
TitleCrystal structure de novo designed fullerene organizing 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 / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsPaul, J. / Acharya, R. / Kim, K.-H. / Kim, Y.H. / Kim, N.H. / Grigoryan, G. / DeGardo, W.F.
Funding support India, 1items
OrganizationGrant numberCountry
DBT India India
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 1.1Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _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

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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
Water36020
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_545-x,-y-1,z1
Buried area5370 Å2
ΔGint-50 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.710, 41.710, 67.230
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.: 20 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M N-(2-Acetamido)iminodiacetic acid, N-(Carbamoylmethyl)iminodiacetic acid (ADA) buffer

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.542 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Jan 14, 2015
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 6255 / % possible obs: 94.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.8 / % possible all: 69.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S0R

3s0r


Resolution: 1.761→24.608 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 603 10.18 %
Rwork0.2027 --
obs0.2064 5916 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.761→24.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 60 20 526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007536
X-RAY DIFFRACTIONf_angle_d0.828778
X-RAY DIFFRACTIONf_dihedral_angle_d17.975166
X-RAY DIFFRACTIONf_chiral_restr0.05470
X-RAY DIFFRACTIONf_plane_restr0.00480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7609-1.83140.326640.2815640X-RAY DIFFRACTION49
1.8314-1.91470.24631150.24071008X-RAY DIFFRACTION78
1.9147-2.01560.27721480.23311246X-RAY DIFFRACTION97
2.0156-2.14180.28091420.20171286X-RAY DIFFRACTION100
2.1418-2.30710.22921450.18351298X-RAY DIFFRACTION99
2.3071-2.53910.22791470.20841272X-RAY DIFFRACTION100
2.5391-2.9060.20151420.19391295X-RAY DIFFRACTION100
2.906-3.65930.23691480.20431296X-RAY DIFFRACTION100
3.6593-24.61040.2421540.19531286X-RAY DIFFRACTION100
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)
10.4948-0.2164-0.32240.3439-0.00250.28750.0933-0.07290.04520.1341-0.1163-0.0878-0.28030.0663-0.00310.192-0.02240.01570.17410.00640.182316.4414-19.68183.3308
20.33080.13460.01570.41150.0530.10760.03170.1590.04980.01090.0164-0.08710.02820.25740.00040.1662-0.0034-0.0230.1919-0.01910.17729.591-11.5142.671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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