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- PDB-5y45: Crystal structure of a collagen-like peptide with interruption se... -

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Basic information

Entry
Database: PDB / ID: 5y45
TitleCrystal structure of a collagen-like peptide with interruption sequence
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / interruption sequence
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.03 Å
AuthorsXu, T. / Liu, J.
CitationJournal: Biochemistry / Year: 2018
Title: Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.
Authors: Xu, T. / Zhou, C.Z. / Xiao, J. / Liu, J.
History
DepositionAug 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 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

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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
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)14,7226
Polymers14,7226
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-59 kcal/mol
Surface area8520 Å2
Unit cell
Length a, b, c (Å)13.750, 45.440, 77.630
Angle α, β, γ (deg.)90.000, 90.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2453.616 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 1.65 Å3/Da / Density % sol: 25.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M HEPES pH 7.0, 30% v/v Jeffamine, M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.03→45.44 Å / Num. obs: 42193 / % possible obs: 94.39 % / Redundancy: 5.8 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimlessdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata collection
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.03→45.44 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.141 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 2185 4.9 %RANDOM
Rwork0.1441 ---
obs0.1457 42193 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.86 Å2 / Biso mean: 9.322 Å2 / Biso min: 3.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0.38 Å2
2---0.11 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.03→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 9 238 1291
Biso mean--10.51 15.76 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021305
X-RAY DIFFRACTIONr_bond_other_d0.0030.021067
X-RAY DIFFRACTIONr_angle_refined_deg2.5532.5331938
X-RAY DIFFRACTIONr_angle_other_deg1.51532691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4331520
X-RAY DIFFRACTIONr_chiral_restr0.090.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.031420
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0264
X-RAY DIFFRACTIONr_rigid_bond_restr1.74132372
X-RAY DIFFRACTIONr_sphericity_free15.079598
X-RAY DIFFRACTIONr_sphericity_bonded6.70752391
LS refinement shellResolution: 1.032→1.059 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 127 -
Rwork0.278 3035 -
all-3162 -
obs--89.22 %

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