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- PDB-3wn8: Crystal Structure of Collagen-Model Peptide, (POG)3-PRG-(POG)4 -

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Basic information

Entry
Database: PDB / ID: 3wn8
TitleCrystal Structure of Collagen-Model Peptide, (POG)3-PRG-(POG)4
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen-helix / HSP47 Binding
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsOkuyama, K. / Haga, M. / Noguchi, K. / Tanaka, T.
CitationJournal: Biopolymers / Year: 2014
Title: Preferred side-chain conformation of arginine residues in a triple-helical structure.
Authors: Okuyama, K. / Haga, M. / Noguchi, K. / Tanaka, T.
History
DepositionDec 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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


Theoretical massNumber of molelcules
Total (without water)6,6013
Polymers6,6013
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-21 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.285, 19.567, 49.022
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide collagen-like peptide


Mass: 2200.345 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: This peptide appears most frequently in native collagen.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 27.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 15 % PEG 4000, 0.05M Tris-HCl, 0.005M Lithium Sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 21, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→8 Å / Num. obs: 7224 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
CrystalCleardata collection
X-PLORmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4F

1v4f


Resolution: 1.45→8 Å / Num. parameters: 2415 / Num. restraintsaints: 2138 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 369 5 %RANDOM
Rwork0.1408 ---
all-7177 --
obs-6808 85 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 402 / Occupancy sum non hydrogen: 591.5
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms463 0 0 129 592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.45-1.510.197X-RAY DIFFRACTION7536
1.51-1.560.193X-RAY DIFFRACTION6186
1.56-1.620.166X-RAY DIFFRACTION6796
1.62-1.710.162X-RAY DIFFRACTION7066
1.71-1.80.158X-RAY DIFFRACTION6626
1.8-1.920.145X-RAY DIFFRACTION6856

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