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- PDB-1rh4: RH4 DESIGNED RIGHT-HANDED COILED COIL TETRAMER -

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Basic information

Entry
Database: PDB / ID: 1rh4
TitleRH4 DESIGNED RIGHT-HANDED COILED COIL TETRAMER
ComponentsRIGHT-HANDED COILED COIL TETRAMER
KeywordsCOILED COIL / DE NOVO DESIGN
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarbury, P.B. / Plecs, J.J. / Tidor, B. / Alber, T. / Kim, P.S.
Citation
Journal: Science / Year: 1998
Title: High-resolution protein design with backbone freedom.
Authors: Harbury, P.B. / Plecs, J.J. / Tidor, B. / Alber, T. / Kim, P.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Repacking Protein Cores with Backbone Freedom: Structure Prediction for Coiled Coils
Authors: Harbury, P.B. / Tidor, B. / Kim, P.S.
History
DepositionOct 7, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: RIGHT-HANDED COILED COIL TETRAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8184
Polymers3,6381
Non-polymers1803
Water1448
1
A: RIGHT-HANDED COILED COIL TETRAMER
hetero molecules

A: RIGHT-HANDED COILED COIL TETRAMER
hetero molecules

A: RIGHT-HANDED COILED COIL TETRAMER
hetero molecules

A: RIGHT-HANDED COILED COIL TETRAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,27116
Polymers14,5504
Non-polymers72112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area9200 Å2
ΔGint-35 kcal/mol
Surface area7880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.556, 37.556, 53.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein/peptide RIGHT-HANDED COILED COIL TETRAMER


Mass: 3637.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.1
Details: 100MM TRIS PH 8.1 0.3M NABR 20% 2-PROPANOL 20% POLYETHLENE GLYCOL 1450
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
20.3 M1reservoirNaBr
320 %isopropanol1reservoir
420 %PEG14501reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→6 Å / Num. obs: 3175 / % possible obs: 86 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.9→1.98 Å / % possible all: 58.9
Reflection shell
*PLUS
% possible obs: 58.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREDICTED STRUCTURE

Resolution: 1.9→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 263 10 %RANDOM
Rwork0.2 ---
obs0.2 3175 85.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms257 0 12 8 277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.828
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d14.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.883
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.342 22 -
Rwork0.273 210 -
obs--58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg14.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.883
LS refinement shell
*PLUS
Rfactor obs: 0.273

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