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- PDB-6w46: Valine-Containing Collagen Peptide -

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Basic information

Entry
Database: PDB / ID: 6w46
TitleValine-Containing Collagen Peptide
ComponentsCollagen-like peptide
KeywordsBIOSYNTHETIC PROTEIN / Collagen / Triple Helix / CMP / Structural Protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Collagen-like peptide
B: Collagen-like peptide
C: Collagen-like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7927
Polymers8,5443
Non-polymers2484
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.300, 19.680, 40.810
Angle α, β, γ (deg.)90.00, 93.26, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain "A" and (resid 1 through 7 or resid 9...
211(chain "B" and (resid 1 through 7 or resid 9...
311(chain "C" and (resid 1 through 7 or resid 9...

NCS oper:
IDCodeMatrixVector
1given(-0.0522759126536, -0.905102289474, 0.421968096597), (0.90443037263, -0.222063984735, -0.364270898849), (0.423406341498, 0.362598169153, 0.830210598406)6.77279796904, 0.964358896985, -5.85762194294
2given(-0.641700221168, 0.41572602279, 0.644509658678), (-0.423217066403, -0.89276112784, 0.154482631136), (0.639615619617, -0.173635948447, 0.748827360977)2.88110948082, 8.85432434278, -7.12634728573

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Components

#1: Protein/peptide Collagen-like peptide


Mass: 2847.886 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.75 Å3/Da / Density % sol: 29.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Crystallization: 0.01 M Li2SO4 Monohydrate, 0.094 M Tris HCl, 30% PEG 4000 Cryoprotectant: 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.25→37.24 Å / Num. obs: 16476 / % possible obs: 97.47 % / Redundancy: 2.9 % / Biso Wilson estimate: 8.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.08 / Rrim(I) all: 0.141 / Net I/σ(I): 5.7
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 3 % / Rmerge(I) obs: 1.081 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1611 / CC1/2: 0.574 / Rpim(I) all: 0.736 / Rrim(I) all: 1.314 / % possible all: 96.44

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Processing

Software
NameVersionClassification
PHENIX1.18RC2_3794refinement
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.24 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.243
RfactorNum. reflection% reflection
Rfree0.227 1633 9.97 %
Rwork0.187 --
obs0.192 16382 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.25→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms597 0 16 136 749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01693
X-RAY DIFFRACTIONf_angle_d1.338967
X-RAY DIFFRACTIONf_dihedral_angle_d28.096136
X-RAY DIFFRACTIONf_chiral_restr0.06895
X-RAY DIFFRACTIONf_plane_restr0.006124
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 (%)
1.25-1.290.31651250.28121220X-RAY DIFFRACTION97
1.29-1.330.31161410.26391178X-RAY DIFFRACTION95
1.33-1.380.29521340.2411196X-RAY DIFFRACTION98
1.38-1.430.29121380.22581185X-RAY DIFFRACTION94
1.43-1.50.27981260.20911244X-RAY DIFFRACTION98
1.5-1.570.23291360.19171188X-RAY DIFFRACTION97
1.57-1.670.23951350.17491246X-RAY DIFFRACTION97
1.67-1.80.24341330.16441226X-RAY DIFFRACTION98
1.8-1.980.22521360.15881256X-RAY DIFFRACTION99
1.98-2.270.20881440.15351245X-RAY DIFFRACTION99
2.27-2.860.21131400.19151262X-RAY DIFFRACTION98
2.86-37.240.18421450.1791303X-RAY DIFFRACTION99

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