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- PDB-6hg7: Crystal structure of a collagen II fragment containing the bindin... -

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Basic information

Entry
Database: PDB / ID: 6hg7
TitleCrystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)
ComponentsCollagen alpha-1(II) chain
KeywordsSTRUCTURAL PROTEIN / collagen helix / collagen-like peptide / collagen II
Function / homology
Function and homology information


collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / Signaling by PDGF / endochondral ossification / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cartilage condensation / inner ear morphogenesis / roof of mouth development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / skeletal system development / central nervous system development / sensory perception of sound / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGebauer, J.M. / Koehler, A. / Dietmar, H. / Gompert, M. / Neundorf, I. / Zaucke, F. / Koch, M. / Baumann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB829/B11 Germany
CitationJournal: Sci Rep / Year: 2018
Title: COMP and TSP-4 interact specifically with the novel GXKGHR motif only found in fibrillar collagens.
Authors: Gebauer, J.M. / Kohler, A. / Dietmar, H. / Gompert, M. / Neundorf, I. / Zaucke, F. / Koch, M. / Baumann, U.
History
DepositionAug 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 19, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_assembly_gen / pdbx_struct_assembly_gen_depositor_info / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_PDB_atom_name / _atom_site_anisotrop.pdbx_PDB_residue_name / _atom_site_anisotrop.pdbx_PDB_residue_no / _atom_site_anisotrop.pdbx_PDB_strand_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen_depositor_info.asym_id_list / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rpim_I_all
Revision 2.2Jan 17, 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 alpha-1(II) chain
B: Collagen alpha-1(II) chain
C: Collagen alpha-1(II) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4034
Polymers10,3073
Non-polymers961
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, CD Spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-38 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.970, 23.640, 107.939
Angle α, β, γ (deg.)90.000, 92.702, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein/peptide Collagen alpha-1(II) chain / Alpha-1 type II collagen


Mass: 3435.760 Da / Num. of mol.: 3
Fragment: C-terminal PEDF/COMP binding region of collagen II
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02458
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Fragment: C-terminal PEDF/COMP binding region of collagen II
Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 1.5 M Ammonium sulphate and 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.98→31.02 Å / Num. obs: 47365 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 9.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.065 / Rrim(I) all: 0.065 / Net I/σ(I): 11.9
Reflection shellResolution: 0.98→0.99 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12828 / CC1/2: 0.949 / Rpim(I) all: 0.541 / Rrim(I) all: 0.899 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4axy

4axy


Resolution: 1→31.02 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.463 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 2211 5.05 %
Rwork0.1519 41566 -
obs0.1536 43777 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.78 Å2
Refinement stepCycle: LAST / Resolution: 1→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 8 164 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154805
X-RAY DIFFRACTIONf_angle_d1.53551104
X-RAY DIFFRACTIONf_chiral_restr0.0677107
X-RAY DIFFRACTIONf_plane_restr0.0063142
X-RAY DIFFRACTIONf_dihedral_angle_d10.2554275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.26821480.23372537X-RAY DIFFRACTION99.11
1.02-1.050.2151580.19522520X-RAY DIFFRACTION99.3
1.05-1.070.23021230.1862608X-RAY DIFFRACTION99.02
1.07-1.10.19191340.17592584X-RAY DIFFRACTION99.89
1.1-1.130.1891530.15422581X-RAY DIFFRACTION99.89
1.13-1.170.1491400.13932573X-RAY DIFFRACTION99.93
1.17-1.210.18091310.13322601X-RAY DIFFRACTION99.82
1.21-1.260.14231410.13372580X-RAY DIFFRACTION99.52
1.26-1.320.18321520.13132592X-RAY DIFFRACTION99.6
1.32-1.390.15441310.12462595X-RAY DIFFRACTION99.53
1.39-1.470.1831310.12882584X-RAY DIFFRACTION98.91
1.47-1.590.17611270.13832629X-RAY DIFFRACTION99.6
1.59-1.750.15861440.13112573X-RAY DIFFRACTION99.6
1.75-20.17221310.14092652X-RAY DIFFRACTION99.68
2-2.520.17361240.14542636X-RAY DIFFRACTION99.46
2.52-31.040.21831430.17362721X-RAY DIFFRACTION99.1

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