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- PDB-3he5: Heterospecific coiled-coil pair SYNZIP2:SYNZIP1 -

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Basic information

Entry
Database: PDB / ID: 3he5
TitleHeterospecific coiled-coil pair SYNZIP2:SYNZIP1
Components
  • SYNZIP1
  • SYNZIP2
KeywordsDE NOVO PROTEIN / heterodimeric coiled-coil
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsReinke, A.W. / Grant, R.A. / Keating, A.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering.
Authors: Reinke, A.W. / Grant, R.A. / Keating, A.E.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: SYNZIP1
B: SYNZIP2
C: SYNZIP1
D: SYNZIP2
E: SYNZIP1
F: SYNZIP2


Theoretical massNumber of molelcules
Total (without water)35,3206
Polymers35,3206
Non-polymers00
Water2,108117
1
A: SYNZIP1
B: SYNZIP2


Theoretical massNumber of molelcules
Total (without water)11,7732
Polymers11,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-24 kcal/mol
Surface area7120 Å2
MethodPISA
2
C: SYNZIP1
D: SYNZIP2


Theoretical massNumber of molelcules
Total (without water)11,7732
Polymers11,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-23 kcal/mol
Surface area7070 Å2
MethodPISA
3
E: SYNZIP1
F: SYNZIP2


Theoretical massNumber of molelcules
Total (without water)11,7732
Polymers11,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-24 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.905, 49.905, 113.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide SYNZIP1


Mass: 5659.444 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): RP3098
#2: Protein SYNZIP2


Mass: 6113.897 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): RP3098
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 45% MPD, 100mM TRIS, 160 mM ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 19, 2008 / Details: VariMaxHR
RadiationMonochromator: VariMaxHR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.392
ReflectionResolution: 1.75→28.43 Å / Num. obs: 31354 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rsym value: 0.038 / Χ2: 0.979 / Net I/σ(I): 42.868
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.294 / Num. unique all: 2903 / Χ2: 0.53 / % possible all: 90.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→28.43 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.663 / σ(F): 2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.228 1598 5.1 %
Rwork0.19 --
obs0.192 31325 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.126 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 63.98 Å2 / Biso mean: 33.214 Å2 / Biso min: 20.48 Å2
Baniso -1Baniso -2Baniso -3
1-4.538 Å2-0 Å2-0 Å2
2--4.538 Å2-0 Å2
3----9.076 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 0 117 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062320
X-RAY DIFFRACTIONf_angle_d0.8123090
X-RAY DIFFRACTIONf_chiral_restr0.048359
X-RAY DIFFRACTIONf_plane_restr0.002402
X-RAY DIFFRACTIONf_dihedral_angle_d16.797950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.7860.328880.33616391727
1.786-1.8280.321130.30217911904
1.828-1.8730.29900.30918991989
1.873-1.9240.2921020.27918971999
1.924-1.9810.288860.28319021988
1.981-2.0450.2771030.26318591962
2.045-2.1180.2661000.24918931993
2.118-2.2030.2731000.23419092009
2.203-2.3030.2421030.22518751978
2.303-2.4240.2851050.22219032008
2.424-2.5760.2531060.21618761982
2.576-2.7740.2171020.20219052007
2.774-3.0530.2211020.18618851987
3.053-3.4950.1931050.16418841989
3.495-4.40.148920.11218281920
4.4-28.4320.266900.17417931883

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