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- PDB-3v86: Computational Design of a Protein Crystal -

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Basic information

Entry
Database: PDB / ID: 3v86
TitleComputational Design of a Protein Crystal
ComponentsDe novo design helix
KeywordsDE NOVO PROTEIN / Computational Design of a protein Crystal / Helical Coil / De novo designed helix
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsAcharya, R. / North, B. / Saven, J. / DeGrado, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Computational design of a protein crystal.
Authors: Lanci, C.J. / Macdermaid, C.M. / Kang, S.G. / Acharya, R. / North, B. / Yang, X. / Qiu, X.J. / Degrado, W.F. / Saven, J.G.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 13, 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: De novo design helix


Theoretical massNumber of molelcules
Total (without water)3,1721
Polymers3,1721
Non-polymers00
Water00
1
A: De novo design helix

A: De novo design helix

A: De novo design helix


Theoretical massNumber of molelcules
Total (without water)9,5153
Polymers9,5153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3340 Å2
ΔGint-28 kcal/mol
Surface area5470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.470, 35.470, 40.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein/peptide De novo design helix


Mass: 3171.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized, De novo design protein

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10mg/ml peptide solution, well solution, 0.01M Cobalt(II) Chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.505
ReflectionResolution: 2.89→40.16 Å / Num. all: 741 / Num. obs: 711 / % possible obs: 95.95 % / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Biso Wilson estimate: 51.38 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.5
Reflection shellResolution: 2.89→3.04 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 11.8 / Num. unique all: 86 / % possible all: 78

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine model generated from 1COI

1coi


Resolution: 2.91→40 Å / Isotropic thermal model: 18.8 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: Engh & Huber
Details: REFINED TWIN FRACTION IS 0.505 AND TWIN LAW IS -H, -K, L, USED PROTOCOL IMPLEMENTED IN SHELXL
RfactorNum. reflection% reflectionSelection details
Rfree0.216 75 -RANDOM
Rwork0.1752 ---
all0.1775 665 --
obs-651 97.89 %-
Refinement stepCycle: LAST / Resolution: 2.91→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms222 0 0 0 222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.013
X-RAY DIFFRACTIONs_from_restr_planes0.0179
X-RAY DIFFRACTIONt_angle_deg0.015
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.168
LS refinement shellResolution: 2.91→3.04 Å
RfactorNum. reflection% reflection
Rwork0.194 --
obs-71 82.6 %

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