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- PDB-1byz: DESIGNED PEPTIDE ALPHA-1, P1 FORM -

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Basic information

Entry
Database: PDB / ID: 1byz
TitleDESIGNED PEPTIDE ALPHA-1, P1 FORM
ComponentsPROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
KeywordsDE NOVO PROTEIN / HELICAL BILAYER / BIOMATERIAL
Function / homologyETHANOLAMINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.9 Å
AuthorsPrive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1999
Title: Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle.
Authors: Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D.
#1: Journal: Protein Sci. / Year: 1999
Title: Centrosymmetric Bilayers in the 0.75A 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.
#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. / De Grado, W.F.
History
DepositionOct 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4May 30, 2018Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Source and taxonomy / Structure summary
Category: entity / exptl_crystal / pdbx_entity_src_syn
Item: _entity.src_method / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
B: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
C: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
D: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,39711
Polymers5,7674
Non-polymers6307
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.846, 20.909, 27.057
Angle α, β, γ (deg.)102.40, 95.33, 119.62
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")


Mass: 1441.775 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: N TERMINI ARE ACETYLATED / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsMPD 513 IS BUILT IN TWO OVERLAPPING CONFORMATIONS. ALL THE WATERS ARE IN SINGLE SITES.

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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: 1.69 Å3/Da / Density % sol: 27.13 % / Description: SNB SUCCESS RATE WAS 5%.
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 91% 2-METHYL-2,4-PENTANEDIOL, 78mM TRIETHANOLAMINE-HCL pH8, 52mM ETHANOLAMINE-HCL pH9.75, pH 8.0, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Details: drop consists of equal volume of peptide and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlpeptide1drop
278 mMtriethanolamine-HCl1reservoir
352 mMethanolamine-HCl1reservoir
491 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1994
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.9→25.7 Å / Num. obs: 23681 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 0.9→0.93 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.141 / % possible all: 36
Reflection
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 25.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 36 % / Num. unique obs: 1011 / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
SHAKEmodel building
SnB(SNB 1.5) MILLERphasing
SHELXLrefinement
SHELXL-97refinement
DENZO(DENZO)data reduction
SCALEPACK(DENZO)data scaling
RefinementMethod to determine structure: DIRECT METHODS
Starting model: 448 RANDOM ATOMS

Resolution: 0.9→25.7 Å / Num. parameters: 4695 / Num. restraintsaints: 5898 / Cross valid method: FREE R / σ(F): 2
StereochEM target val spec case: ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS
Stereochemistry target values: ENGH AND HUBER
Details: MORE LOW-OCCUPANCY DISCRETE DISORDER COULD BE BUILT FOR SOLVENT AND PEPTIDE, BUT WOULD EXCESSIVELY INCREASE THE NUMBER OF REFINEABLE PARAMETERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.105 2368 10 %EVERY TENTH REFLECTION SAME TEST SET FOR SHELXL-93 AND SHELXL-97
all0.086 23681 --
obs0.085 -85.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 544 / Occupancy sum non hydrogen: 478.97
Refinement stepCycle: LAST / Resolution: 0.9→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 41 30 479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.192
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.108
Software
*PLUS
Name: SHELXL / Version: 93 and 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.9 Å / Rfactor obs: 0.086
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.061.9
X-RAY DIFFRACTIONs_chiral_restr0.20.065
LS refinement shell
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 1.01 Å / Rfactor Rwork: 0.164

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