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- PDB-6w47: Peptoid-Containing Collagen Peptide -

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Basic information

Entry
Database: PDB / ID: 6w47
TitlePeptoid-Containing Collagen Peptide
ComponentsCollagen-like peptide
KeywordsBIOSYNTHETIC PROTEIN / Collagen / Triple Helix / CMP / Peptoid / STRUCTURAL PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsChenoweth, D.M. / Melton, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)Penn MRSEC Grant No. DMR-1720530 United States
CitationJournal: Chem Sci / Year: 2020
Title: Rules for the design of aza-glycine stabilized triple-helical collagen peptides.
Authors: Melton, S.D. / Brackhahn, E.A.E. / Orlin, S.J. / Jin, P. / Chenoweth, D.M.
History
DepositionMar 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen-like peptide
B: Collagen-like peptide
C: Collagen-like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3334
Polymers7,2713
Non-polymers621
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-22 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.679, 19.556, 37.528
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid 2 through 7 or resid 9 through 26))
211(chain B and (resid 2 through 7 or resid 9 through 26))
311(chain C and (resid 2 through 7 or resid 9 through 26))

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Components

#1: Protein/peptide Collagen-like peptide


Mass: 2423.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.57 Å3/Da / Density % sol: 21.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Crystallization: 0.2 M Potassium formate, 20% PEG 3350 Cryoprotectant: 20% Glycercol
Temp details: After

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.15→37.07 Å / Num. obs: 15857 / % possible obs: 95.75 % / Redundancy: 4.6 % / Biso Wilson estimate: 8.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.072 / Rrim(I) all: 0.122 / Net I/σ(I): 9.4
Reflection shellResolution: 1.15→1.191 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1215 / CC1/2: 0.823 / Rpim(I) all: 0.53 / Rrim(I) all: 0.796 / % possible all: 75.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.2 Å31.3 Å
Translation1.2 Å31.3 Å

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Processing

Software
NameVersionClassification
PHENIX1.18RC2_3794refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABN

3abn


Resolution: 1.15→37.07 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.362
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.217 1580 10 %
Rwork0.183 --
obs0.187 15798 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.1 Å2
Refinement stepCycle: LAST / Resolution: 1.15→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 4 82 586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011547
X-RAY DIFFRACTIONf_angle_d1.361751
X-RAY DIFFRACTIONf_dihedral_angle_d14.043106
X-RAY DIFFRACTIONf_chiral_restr0.0674
X-RAY DIFFRACTIONf_plane_restr0.00595
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.190.27411090.2703975X-RAY DIFFRACTION75
1.19-1.230.26851410.22111277X-RAY DIFFRACTION94
1.23-1.280.23551470.21471315X-RAY DIFFRACTION99
1.28-1.340.23421460.19641310X-RAY DIFFRACTION98
1.34-1.410.21521490.18071330X-RAY DIFFRACTION99
1.41-1.50.20471470.18851324X-RAY DIFFRACTION98
1.5-1.610.25211460.18161322X-RAY DIFFRACTION99
1.61-1.770.20841480.17761328X-RAY DIFFRACTION98
1.77-2.030.23751470.17911314X-RAY DIFFRACTION98
2.03-2.560.19211480.16611351X-RAY DIFFRACTION98
2.56-37.070.20281520.17561372X-RAY DIFFRACTION96

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