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- PDB-4dmt: Crystal structure of a VWF binding collagen III derived triple he... -

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Basic information

Entry
Database: PDB / ID: 4dmt
TitleCrystal structure of a VWF binding collagen III derived triple helical peptide
ComponentsCollagen III derived peptide
KeywordsSTRUCTURAL PROTEIN / collagen triple helix / Von willebrand factor
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsBrondijk, T.H.C. / Huizinga, E.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Implications for collagen I chain registry from the structure of the collagen von Willebrand factor A3 domain complex.
Authors: Brondijk, T.H. / Bihan, D. / Farndale, R.W. / Huizinga, E.G.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_site
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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen III derived peptide
B: Collagen III derived peptide
C: Collagen III derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9497
Polymers8,5803
Non-polymers3684
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-31 kcal/mol
Surface area5960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.330, 24.430, 39.320
Angle α, β, γ (deg.)90.00, 103.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Collagen III derived peptide


Mass: 2860.123 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: synthetic peptide covers part of human collagen III sequence
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.71 Å3/Da / Density % sol: 27.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.95-1.0 M ammonium tartrate , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.39→38.29 Å / Num. all: 11914 / Num. obs: 11914 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 6.9 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.8
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1721 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V7H poly-ala

1v7h


Resolution: 1.39→38.29 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.898 / SU ML: 0.034 / Isotropic thermal model: anisotrpic / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14466 570 4.8 %RANDOM
Rwork0.10671 ---
obs0.10847 11334 99.78 %-
all-11334 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.33 Å2
2---0.07 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.39→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 24 157 787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021686
X-RAY DIFFRACTIONr_bond_other_d0.0030.02520
X-RAY DIFFRACTIONr_angle_refined_deg1.942.403965
X-RAY DIFFRACTIONr_angle_other_deg1.00231228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.922591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.092209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1041532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.093153
X-RAY DIFFRACTIONr_chiral_restr0.0920.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0272
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_it0.9211.5481
X-RAY DIFFRACTIONr_mcbond_other0.2841.5167
X-RAY DIFFRACTIONr_mcangle_it1.3822786
X-RAY DIFFRACTIONr_scbond_it2.133205
X-RAY DIFFRACTIONr_scangle_it3.2454.5178
X-RAY DIFFRACTIONr_rigid_bond_restr0.80731204
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 48 -
Rwork0.15 836 -
obs--99.1 %

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