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

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Basic information

Entry
Database: PDB / ID: 4cnb
TitleStructure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus - Crystal form 2
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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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: 1.95 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 1.3Jun 18, 2014Group: Other
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROXIMAL THREAD MATRIX PROTEIN 1
B: PROXIMAL THREAD MATRIX PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3197
Polymers97,9412
Non-polymers3785
Water5,999333
1
A: PROXIMAL THREAD MATRIX PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1914
Polymers48,9701
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROXIMAL THREAD MATRIX PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1283
Polymers48,9701
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.010, 62.280, 122.560
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9117, -0.002427, 0.4108), (-0.002011, -1, -0.001444), (0.4108, 0.000491, -0.9117)
Vector: -10.03, -27.13, 47.2)

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Components

#1: Protein PROXIMAL THREAD MATRIX PROTEIN 1


Mass: 48970.336 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.36 Å3/Da / Density % sol: 47.91 % / Description: NONE
Crystal growpH: 4.6
Details: 28% 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: Sep 5, 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: 1.95→55.3 Å / Num. obs: 63031 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 17.69 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.9 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CN8

4cn8


Resolution: 1.95→38.977 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 3151 5 %
Rwork0.2135 --
obs0.2156 63024 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 22 333 6271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076031
X-RAY DIFFRACTIONf_angle_d0.9968109
X-RAY DIFFRACTIONf_dihedral_angle_d14.4642226
X-RAY DIFFRACTIONf_chiral_restr0.058934
X-RAY DIFFRACTIONf_plane_restr0.0041053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97910.40241340.33912542X-RAY DIFFRACTION93
1.9791-2.010.29611360.30482595X-RAY DIFFRACTION93
2.01-2.0430.34811330.28492522X-RAY DIFFRACTION93
2.043-2.07820.31821340.27662549X-RAY DIFFRACTION93
2.0782-2.1160.29031350.28242554X-RAY DIFFRACTION94
2.116-2.15670.30111400.26492660X-RAY DIFFRACTION96
2.1567-2.20070.30451400.24882657X-RAY DIFFRACTION97
2.2007-2.24860.31141390.2472645X-RAY DIFFRACTION97
2.2486-2.30090.27131390.22842651X-RAY DIFFRACTION96
2.3009-2.35840.26591400.22712648X-RAY DIFFRACTION97
2.3584-2.42210.26971380.2142617X-RAY DIFFRACTION96
2.4221-2.49340.27391410.21022679X-RAY DIFFRACTION96
2.4934-2.57390.26951390.20482643X-RAY DIFFRACTION96
2.5739-2.66580.26551370.20542629X-RAY DIFFRACTION96
2.6658-2.77260.25591380.20422621X-RAY DIFFRACTION96
2.7726-2.89870.23641390.19552636X-RAY DIFFRACTION95
2.8987-3.05150.24421380.19432631X-RAY DIFFRACTION95
3.0515-3.24260.27431380.19952619X-RAY DIFFRACTION95
3.2426-3.49280.20271370.18492608X-RAY DIFFRACTION94
3.4928-3.8440.22211360.17552583X-RAY DIFFRACTION93
3.844-4.39960.19361350.16972570X-RAY DIFFRACTION92
4.3996-5.54050.18831350.18222546X-RAY DIFFRACTION91
5.5405-38.98480.26211300.22122468X-RAY DIFFRACTION86

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