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- PDB-3tq2: Merohedral twinning in protein crystals revealed a new synthetic ... -

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Basic information

Entry
Database: PDB / ID: 3tq2
TitleMerohedral twinning in protein crystals revealed a new synthetic three helix bundle motif
ComponentsKE1
KeywordsDE NOVO PROTEIN / Parallel three helix bundle
Biological speciesSynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGeremia, S. / De March, M.
Citation
Journal: Proteins / Year: 2023
Title: Analysis of the crystal structure of a parallel three-stranded coiled coil.
Authors: de March, M. / Hickey, N. / Geremia, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A coiled-coil motif that sequesters ions to the hydrophobic core.
Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0832
Polymers3,9871
Non-polymers961
Water50428
1
A: KE1
hetero molecules

A: KE1
hetero molecules

A: KE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2496
Polymers11,9613
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4790 Å2
ΔGint-47 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.365, 22.365, 51.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-36-

SO4

21A-36-

SO4

31A-54-

HOH

41A-60-

HOH

51A-61-

HOH

61A-63-

HOH

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Components

#1: Protein/peptide KE1


Mass: 3986.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid Phase Chemistry / Source: (synth.) Synthetic (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 1.8-2.5M ammonium sulfate, 1.5-3% w/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONELETTRA 5.2R11
ROTATING ANODEOTHER21.54
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 19, 2008
Nonius Kappa CCD2CCDMay 8, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541
ReflectionResolution: 1.1→50 Å / Num. all: 10855 / Num. obs: 30622 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.74 / % possible all: 85.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a 35 Poly-Ala model

Resolution: 1.1→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.185 543 RANDOM
Rwork0.158 --
all0.21 10855 -
obs0.188 30622 -
Refinement stepCycle: LAST / Resolution: 1.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms279 0 3 28 310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg0.032
X-RAY DIFFRACTIONr_bond_refined_d0.017

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