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- PDB-1fe6: CRYSTAL STRUCTURE OF A NATURALLY OCCURING PARALLEL RIGHT-HANDED C... -

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Basic information

Entry
Database: PDB / ID: 1fe6
TitleCRYSTAL STRUCTURE OF A NATURALLY OCCURING PARALLEL RIGHT-HANDED COILED-COIL TETRAMER
ComponentsTETRABRACHION
KeywordsPROTEIN BINDING / right handed coiled coil
Function / homologyTetrabrachion / Tetrabrachion / Tetrabrachion, parallel right-handed coiled coil domain / Tetrabrachion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / membrane / Tetrabrachion
Function and homology information
Biological speciesStaphylothermus marinus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsStetefeld, J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer.
Authors: Stetefeld, J. / Jenny, M. / Schulthess, T. / Landwehr, R. / Engel, J. / Kammerer, R.A.
History
DepositionJul 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TETRABRACHION
B: TETRABRACHION
C: TETRABRACHION
D: TETRABRACHION


Theoretical massNumber of molelcules
Total (without water)23,3704
Polymers23,3704
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-79 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.243, 110.243, 70.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
TETRABRACHION


Mass: 5842.614 Da / Num. of mol.: 4 / Fragment: RIGHT HANDED COILED COIL / Source method: isolated from a natural source / Source: (natural) Staphylothermus marinus (archaea) / References: UniProt: Q54436
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 5.32 Å3/Da / Density % sol: 76.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.8 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
3200 mMTris-HCl1reservoirpH7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 25 Å2
Reflection shellResolution: 1.8→30 Å
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 46116 / % possible obs: 100 % / Num. measured all: 854694 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.8→6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1170888.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4520 10.1 %RANDOM
Rwork0.198 ---
obs0.198 44935 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 130.3 Å2 / ksol: 0.714 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.48 Å20 Å2
2--1.72 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 0 277 1895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 6642 10.4 %
Rwork0.232 773 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.1977 / Rfactor Rfree: 0.2165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.72 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.72
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.65
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.232

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