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Basic information

Entry
Database: PDB / ID: 4ndl
TitleComputational design and experimental verification of a symmetric homodimer
ComponentsENH-c2b, computational designed homodimer
KeywordsDE NOVO PROTEIN / helix-turn-helix
Function / homologyHomeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMou, Y. / Huang, P.S. / Hsu, F.C. / Huang, S.J. / Mayo, S.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Computational design and experimental verification of a symmetric protein homodimer.
Authors: Mou, Y. / Huang, P.S. / Hsu, F.C. / Huang, S.J. / Mayo, S.L.
History
DepositionOct 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Feb 28, 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
B: ENH-c2b, computational designed homodimer
A: ENH-c2b, computational designed homodimer
C: ENH-c2b, computational designed homodimer


Theoretical massNumber of molelcules
Total (without water)26,5473
Polymers26,5473
Non-polymers00
Water181
1
B: ENH-c2b, computational designed homodimer


Theoretical massNumber of molelcules
Total (without water)8,8491
Polymers8,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ENH-c2b, computational designed homodimer


Theoretical massNumber of molelcules
Total (without water)8,8491
Polymers8,8491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENH-c2b, computational designed homodimer


Theoretical massNumber of molelcules
Total (without water)8,8491
Polymers8,8491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.550, 167.770, 29.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ENH-c2b, computational designed homodimer


Mass: 8848.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 298 K / pH: 7
Details: 1% w/v tryptone, 20% w/v polyethylene glycerol 3350, 0.05 M HEPES sodium, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.915
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.2→24.6 Å / Num. obs: 5697

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→24.6 Å / SU ML: 0.46 / σ(F): 1.53 / Phase error: 31.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3585 130 4.38 %
Rwork0.312 --
obs0.313 2968 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 0 1 1071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091099
X-RAY DIFFRACTIONf_angle_d1.7721489
X-RAY DIFFRACTIONf_dihedral_angle_d16.371372
X-RAY DIFFRACTIONf_chiral_restr0.075155
X-RAY DIFFRACTIONf_plane_restr0.009188

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