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- PDB-3p46: Integrin binding collagen peptide -

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Basic information

Entry
Database: PDB / ID: 3p46
TitleIntegrin binding collagen peptide
ComponentsSynthetic collagen peptide
KeywordsDE NOVO PROTEIN / collagen / integrin recognition / integrin alpha 1 beta 1
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsMcEwan, P.A. / Emsley, J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: End-stapled homo and hetero collagen triple helices: a click chemistry approach.
Authors: Byrne, C. / McEwan, P.A. / Emsley, J. / Fischer, P.M. / Chan, W.C.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,9553
Polymers4,9553
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-14 kcal/mol
Surface area3340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.018, 17.288, 26.048
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Synthetic collagen peptide


Mass: 1651.754 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 50 mM Tris pH 7.5, 0.1 M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 13, 2008
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→22.37 Å / Num. all: 4110 / Num. obs: 4110 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementResolution: 1.7→22.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.971 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24016 195 4.7 %RANDOM
Rwork0.19624 ---
obs0.19837 3914 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.06 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms350 0 0 80 430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.021374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8162.471533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.143551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.652303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0041512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1650.254
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.03324
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3261.5284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9762455
X-RAY DIFFRACTIONr_scbond_it3.225390
X-RAY DIFFRACTIONr_scangle_it5.5344.578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 9 -
Rwork0.382 210 -
obs--67.38 %

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