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- PDB-3al1: DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM -

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Basic information

Entry
Database: PDB / ID: 3al1
TitleDESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM
ComponentsPROTEIN (D, L-ALPHA-1)
KeywordsSTRUCTURAL PROTEIN / HELICAL BILAYER / BIOMATERIAL / CENTRIC / RACEMIC
Function / homologyETHANOLAMINE
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.75 Å
AuthorsPatterson, W.R. / Anderson, D.H. / Degrado, W.F. / Cascio, D. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1999
Title: Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
Authors: Patterson, W.R. / Anderson, D.H. / DeGrado, W.F. / Cascio, D. / Eisenberg, D.
#1: Journal: To be Published
Title: Packed Protein Bilayers in the 0.90A Resolution Structure of a Designed Alpha Helical Bundle
Authors: Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D.
#2: Journal: Science / Year: 1990
Title: Crystal Structure of Alpha-1: Implications for Protein Design
Authors: Hill, C.P. / Anderson, D.H. / Wesson, L. / Degrado, W.F. / Eisenberg, D.
#3: Journal: Proteins / Year: 1986
Title: The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide
Authors: Eisenberg, D. / Wilcox, W. / Eshita, S.M. / Pryciak, P.M. / Ho, S.P.
History
DepositionOct 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine / Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (D, L-ALPHA-1)
B: PROTEIN (D, L-ALPHA-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1245
Polymers2,8842
Non-polymers2403
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.544, 20.859, 26.055
Angle α, β, γ (deg.)101.16, 97.03, 118.06
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide PROTEIN (D, L-ALPHA-1)


Mass: 1441.775 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE WAS SYNTHESIZED VIA SOLID PHASE SYNTHESIS AND DESIGNED TO BE AN AMPHIPHILIC HELIX
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.61 Å3/Da / Density % sol: 14.8 %
Description: THERE IS NO REDUNDANCY IN THE DATA SET BEYOND 1.28A RESOLUTION; RSYM CAN BE EVALUATED ONLY FOR 18-1.28A. DATA REDUNDANCY IN 18-1.28A SHELL IS 2.51
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: EQUAL VOLUMES OF 10 MG/ML D-ALPHA-1 AND 10 MG/ML L-ALPHA-1 WERE MIXED IMMEDIATELY BEFORE CRYSTALLIZATION. THE RESERVOIR SOLUTION CONTAINED 90-93% 2-METHYL-2,4-PENTANEDIOL, 0.075 M ...Details: EQUAL VOLUMES OF 10 MG/ML D-ALPHA-1 AND 10 MG/ML L-ALPHA-1 WERE MIXED IMMEDIATELY BEFORE CRYSTALLIZATION. THE RESERVOIR SOLUTION CONTAINED 90-93% 2-METHYL-2,4-PENTANEDIOL, 0.075 M ETHANOLAMINE HCL PH 9.75, 0.05 M TRIETHANOLAMINE HCL PH 8. THE HANGING DROP CONTAINED EQUAL VOLUMES OF RESERVOIR AND 10 MG/ML D,L MIX ALPHA-1. THE ACIDIC PEPTIDE PARTWAY TITRATES THE BASIC BUFFERS TO REACH THE UNKNOWN RESULTANT PH., vapor diffusion - hanging drop
PH range: 8-9.75
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
190-93 %MPD1reservoir
275 mMethanolamine-HCl1reservoirpH9.75
350 mMTEA-HCl1reservoirpH8.0
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.75→18 Å / Num. obs: 33573 / % possible obs: 71.5 % / Observed criterion σ(I): 1 / Redundancy: 1.4 % / Rsym value: 10 / Net I/σ(I): 10.6
Reflection shellResolution: 0.75→0.78 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2 / % possible all: 24.9
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 24.9 % / Num. unique obs: 1172

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.75→18 Å / Num. parameters: 2939 / Num. restraintsaints: 4291 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: GLU 108 CONFORMATION C CARBOXYLATE HAS A STIFF PLANARITY RESTRAINT. ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS.
Stereochemistry target values: ENGH AND HUBER
Details: STRUCTURE WAS REDETERMINED WITH SHAKE AND BAKE BECAUSE THE REFINEMENT WAS STUCK AT R ABOUT 21%. THE SNB RESULT CONFIRMED THE SHELXS STRUCTURE. SAME TEST SET WAS USED FOR SHELXL-93 AND -97. ...Details: STRUCTURE WAS REDETERMINED WITH SHAKE AND BAKE BECAUSE THE REFINEMENT WAS STUCK AT R ABOUT 21%. THE SNB RESULT CONFIRMED THE SHELXS STRUCTURE. SAME TEST SET WAS USED FOR SHELXL-93 AND -97. SAME RESTRAINTS WERE CARRIED ALONG INTO SHELXL-97; THERE WAS NO DFIX/DANG DISTINCTION. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ONLY 1%. IN THIS REFINEMENT, THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 22.6 - 14.5%
RfactorNum. reflection% reflectionSelection details
Rfree0.145 3329 10 %EVERY TENTH REFLECTION
all0.131 33290 --
obs0.13 -71.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 250.04 / Occupancy sum non hydrogen: 237.88
Refinement stepCycle: LAST / Resolution: 0.75→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms204 0 16 21 241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.038
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.028
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.086
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.04
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.13 / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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