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- PDB-4z1r: Crystal structure of collagen-like peptide at 1.27 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4z1r
TitleCrystal structure of collagen-like peptide at 1.27 Angstrom resolution
ComponentsCollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / Collagen / triple helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsPlonska-Brzezinska, M.E. / Czyrko, J. / Brus, D.M. / Imierska, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2011/01/B/ST5/06051 Poland
CitationJournal: Rsc Adv / Year: 2015
Title: Triple helical collagen-like peptide interactions with selected polyphenolic compounds.
Authors: Plonska-Brzezinska, M.E. / Bobrowska, D.M. / Sharma, A. / Rodziewicz, P. / Tomczyk, M. / Czyrko, J. / Brzezinski, K.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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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)8,1153
Polymers8,1153
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-24 kcal/mol
Surface area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.573, 13.939, 24.981
Angle α, β, γ (deg.)90.000, 94.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Collagen-like peptide


Mass: 2704.854 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.83 Å3/Da / Density % sol: 32.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 400, 5% acetic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionNumber: 60616 / Rmerge(I) obs: 0.052 / Χ2: 0.96 / D res high: 1.27 Å / Num. obs: 16057 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
3.793066310.035
2.693.79113210.039
2.22.69145310.042
1.92.2168710.045
1.71.9191510.057
1.551.7207210.07
1.441.55229010.098
1.351.44245810.113
1.271.35238710.148
ReflectionResolution: 1.27→30 Å / Num. obs: 16057 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 11.523 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.06 / Χ2: 0.962 / Net I/σ(I): 17.15 / Num. measured all: 60616
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.27-1.350.9710.1488.017627254723870.17993.7
1.35-1.440.9950.11311.119656246424580.1399.8
1.44-1.550.9910.09812.639009229122900.113100
1.55-1.70.9950.0716.758162207820720.0899.7
1.7-1.90.9970.05719.427582192019150.06599.7
1.9-2.20.9970.04524.376510168916870.05199.9
2.2-2.690.9980.04225.935518145714530.04899.7
2.69-3.790.9970.03927.74285114211320.04599.1
3.79-300.9970.03527.2222676966630.04195.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CAG

1cag


Resolution: 1.27→28.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.402 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 1044 6.5 %RANDOM
Rwork0.1374 ---
obs0.1396 15012 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 37.07 Å2 / Biso mean: 8.171 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å20.17 Å2
2---0.43 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.27→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms491 0 0 188 679
Biso mean---12.94 -
Num. residues----78
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.018548
X-RAY DIFFRACTIONr_bond_other_d0.0020.017431
X-RAY DIFFRACTIONr_angle_refined_deg2.0312.377807
X-RAY DIFFRACTIONr_angle_other_deg1.09631069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.881577
X-RAY DIFFRACTIONr_chiral_restr0.0850.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.032516
X-RAY DIFFRACTIONr_mcbond_it1.1050.641312
X-RAY DIFFRACTIONr_mcbond_other1.0950.636311
X-RAY DIFFRACTIONr_mcangle_it1.2580.942387
X-RAY DIFFRACTIONr_rigid_bond_restr1.3263979
X-RAY DIFFRACTIONr_sphericity_free27.85558
X-RAY DIFFRACTIONr_sphericity_bonded7.14351109
LS refinement shellResolution: 1.269→1.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 68 -
Rwork0.137 977 -
all-1045 -
obs--89.09 %

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