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- PDB-4cn8: Structure of proximal thread matrix protein 1 (PTMP1) from the mu... -

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Basic information

Entry
Database: PDB / ID: 4cn8
TitleStructure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus
ComponentsPROXIMAL THREAD MATRIX PROTEIN 1
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proximal thread matrix protein 1
Similarity search - Component
Biological speciesMYTILUS GALLOPROVINCIALIS (Mediterranean mussel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGertz, M. / Suhre, M.H. / Scheibel, T. / Steegborn, C.
CitationJournal: Nat.Commun. / Year: 2014
Title: Structural and Functional Features of a Collagen-Binding Matrix Protein from the Mussel Byssus.
Authors: Suhre, M.H. / Gertz, M. / Steegborn, C. / Scheibel, T.
History
DepositionJan 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Atomic model
Revision 1.2Mar 26, 2014Group: Atomic model
Revision 1.3Apr 23, 2014Group: Atomic model
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: PROXIMAL THREAD MATRIX PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4246
Polymers49,0111
Non-polymers4125
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.530, 44.540, 85.850
Angle α, β, γ (deg.)90.00, 105.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROXIMAL THREAD MATRIX PROTEIN 1


Mass: 49011.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYTILUS GALLOPROVINCIALIS (Mediterranean mussel)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q8T5C2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.19 Å3/Da / Density % sol: 43.72 % / Description: NONE
Crystal growpH: 4.6
Details: 30% PEG2000-MME, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2012 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.45→56 Å / Num. obs: 15438 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 35.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AOX, 1QC5

1aox

1qc5


Resolution: 2.45→30.832 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 772 5 %
Rwork0.2046 --
obs0.2068 15437 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.2 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 23 39 3061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053062
X-RAY DIFFRACTIONf_angle_d0.8384116
X-RAY DIFFRACTIONf_dihedral_angle_d14.5991129
X-RAY DIFFRACTIONf_chiral_restr0.085471
X-RAY DIFFRACTIONf_plane_restr0.003534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60350.35051100.29412101X-RAY DIFFRACTION84
2.6035-2.80440.32491300.26762471X-RAY DIFFRACTION100
2.8044-3.08630.30591310.24432489X-RAY DIFFRACTION100
3.0863-3.53240.22241310.20812488X-RAY DIFFRACTION100
3.5324-4.44830.21251340.17572543X-RAY DIFFRACTION100
4.4483-30.83410.23191360.17312573X-RAY DIFFRACTION100

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