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- PDB-4bwd: Human short coiled coil protein -

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Basic information

Entry
Database: PDB / ID: 4bwd
TitleHuman short coiled coil protein
ComponentsSHORT COILED-COIL PROTEIN
KeywordsSTRUCTURAL PROTEIN / SCAFFOLD PROTEIN
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / regulation of protein complex stability / positive regulation of macroautophagy / Golgi membrane / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
Short coiled-coil protein / Short coiled-coil protein / Single 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
Similarity search - Domain/homology
Short coiled-coil protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsBehrens, C. / Binotti, B. / Chua, J.J. / Kuhnel, K.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of the Human Short Coiled Coil Protein and Insights Into Scoc-Fez1 Complex Formation.
Authors: Behrens, C. / Binotti, B. / Schmidt, C. / Robinson, C.V. / Chua, J.J.E. / Kuhnel, K.
History
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHORT COILED-COIL PROTEIN
B: SHORT COILED-COIL PROTEIN
C: SHORT COILED-COIL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,1513
Polymers28,1513
Non-polymers00
Water77543
1
A: SHORT COILED-COIL PROTEIN
B: SHORT COILED-COIL PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,7672
Polymers18,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22.5 kcal/mol
Surface area9240 Å2
MethodPISA
2
C: SHORT COILED-COIL PROTEIN

C: SHORT COILED-COIL PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,7672
Polymers18,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2370 Å2
ΔGint-23.5 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.980, 114.750, 93.270
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 SHORT COILED-COIL PROTEIN


Mass: 9383.537 Da / Num. of mol.: 3 / Fragment: COILED COIL DOMAIN, RESIDUES 78-159 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UIL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3 Å3/Da / Density % sol: 59.2 % / Description: NONE
Crystal growpH: 4.6
Details: 0.01 M COBALT CHLORIDE 0.1 M SODIUM ACETATE PH 4.63, 0.7 M 1,6 HEXANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 10743 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 58.67 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.44 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.7 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.702→36.905 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 26.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2601 537 5 %
Rwork0.2188 --
obs0.2209 10738 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.1 Å2
Refinement stepCycle: LAST / Resolution: 2.702→36.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 43 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081384
X-RAY DIFFRACTIONf_angle_d0.9991866
X-RAY DIFFRACTIONf_dihedral_angle_d16.26520
X-RAY DIFFRACTIONf_chiral_restr0.061232
X-RAY DIFFRACTIONf_plane_restr0.003244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.97380.2821300.22582487X-RAY DIFFRACTION99
2.9738-3.40390.27451330.2252528X-RAY DIFFRACTION100
3.4039-4.28750.25611340.2022538X-RAY DIFFRACTION100
4.2875-36.90810.25331400.22652648X-RAY DIFFRACTION100

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