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- PDB-1bb1: CRYSTAL STRUCTURE OF A DESIGNED, THERMOSTABLE HETEROTRIMERIC COIL... -

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Basic information

Entry
Database: PDB / ID: 1bb1
TitleCRYSTAL STRUCTURE OF A DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
Components(DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL) x 3
KeywordsDE NOVO PROTEIN DESIGN / COILED COIL
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsNautiyal, S. / Alber, T.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
Authors: Nautiyal, S. / Alber, T.
#1: Journal: Biochemistry / Year: 1995
Title: A Designed Heterotrimeric Coiled Coil
Authors: Nautiyal, S. / Woolfson, D.N. / King, D.S. / Alber, T.
History
DepositionApr 28, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
B: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
C: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2474
Polymers11,2113
Non-polymers351
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-47 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.930, 35.010, 66.460
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3703.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3839.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#3: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3668.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
350 mM1reservoirMgCl2
425 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 9067 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.036 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 8 / Rsym value: 0.083 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED INDIVIDUAL B'S / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1004 10.9 %RANDOM
Rwork0.208 ---
obs0.208 9134 99.2 %-
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 1 125 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.636
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it2.362
X-RAY DIFFRACTIONx_scbond_it3.582
X-RAY DIFFRACTIONx_scangle_it5.9492.5
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 121 10.6 %
Rwork0.307 984 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAM
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5
LS refinement shell
*PLUS
Rfactor obs: 0.307

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