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- PDB-6vzx: Structure of a Covalently Captured Collagen Triple Helix using Ly... -

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Basic information

Entry
Database: PDB / ID: 6vzx
TitleStructure of a Covalently Captured Collagen Triple Helix using Lysine-Glutamate Pairs
Componentscollagen mimetic peptide
KeywordsBIOSYNTHETIC PROTEIN / collagen mimetic peptide / Triple Helix / isopeptide bond
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsMiller, M.D. / Hulgan, S.A. / Xu, W. / Kosgei, A.J. / Phillips Jr., G.N. / Hartgerink, J.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1709631 United States
Welch FoundationC1557 United States
National Science Foundation (NSF, United States)STC-1231306 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160652 United States
CitationJournal: Biomacromolecules / Year: 2020
Title: Covalent Capture of Collagen Triple Helices Using Lysine-Aspartate and Lysine-Glutamate Pairs.
Authors: Hulgan, S.A.H. / Jalan, A.A. / Li, I.C. / Walker, D.R. / Miller, M.D. / Kosgei, A.J. / Xu, W. / Phillips Jr., G.N. / Hartgerink, J.D.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: collagen mimetic peptide
B: collagen mimetic peptide
C: collagen mimetic peptide


Theoretical massNumber of molelcules
Total (without water)6,6853
Polymers6,6853
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, mass spectrometry confirms the covalent linkage of the three chains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-21 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.835, 14.113, 24.568
Angle α, β, γ (deg.)90.000, 90.350, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-140-

HOH

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Components

#1: Protein/peptide collagen mimetic peptide


Mass: 2228.375 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Fmoc Solid Phase Peptide Chemistry with N-Terminal Acetylation and C-Terminal Amidation
Source: (synth.) synthetic construct (others)
#2: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M sodium formate, 0.1 M BIS-TRIS, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019 / Details: Adjustable focus K-B pair
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.37→33.71 Å / Num. obs: 9559 / % possible obs: 93.5 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.046 / Rrim(I) all: 0.157 / Net I/σ(I): 8.7 / Num. measured all: 107201 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.37-1.416.91.01430904500.7270.4061.0961.759.5
6.12-33.7111.10.07615361380.9980.0260.08116.199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
xia20.5.893-gb176367e-dials-1.14data reduction
DIALS1.14.5-g19190e3b9-releasedata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3t4f

3t4f


Resolution: 1.37→33.71 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 463 4.85 %
Rwork0.1571 9076 -
obs0.1582 9539 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.21 Å2 / Biso mean: 14.0822 Å2 / Biso min: 3.03 Å2
Refinement stepCycle: final / Resolution: 1.37→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 0 145 619
Biso mean---21.29 -
Num. residues----72
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013531
X-RAY DIFFRACTIONf_angle_d1.661747
X-RAY DIFFRACTIONf_dihedral_angle_d11.557280
X-RAY DIFFRACTIONf_chiral_restr0.05271
X-RAY DIFFRACTIONf_plane_restr0.008105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.570.24541240.21742578270280
1.57-1.980.21241630.18231783341100
1.98-33.710.15131760.13433203496100

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