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- PDB-4cn9: structure of proximal thread matrix protein 1 (PTMP1) from the mu... -

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Basic information

Entry
Database: PDB / ID: 4cn9
Titlestructure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus with zinc occupied MIDAS motif
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: 1.9 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 26, 2014Group: Atomic model
Revision 1.2Apr 23, 2014Group: Atomic model
Revision 1.3Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Nov 13, 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)98,94915
Polymers97,9412
Non-polymers1,00813
Water7,170398
1
A: PROXIMAL THREAD MATRIX PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4437
Polymers48,9701
Non-polymers4736
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)49,5068
Polymers48,9701
Non-polymers5357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.540, 63.070, 122.350
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.917, -0.000264, 0.3988), (0.000184, -1, -0.001085), (0.3988, 0.001068, -0.917)
Vector: -9.787, -27.67, 47.62)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 411 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.16 % / 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: 1.283
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.9→43.6 Å / Num. obs: 72516 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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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 4CNB

4cnb


Resolution: 1.9→43.559 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 3626 5 %
Rwork0.1732 --
obs0.175 72507 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 50 398 6496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096218
X-RAY DIFFRACTIONf_angle_d1.0828379
X-RAY DIFFRACTIONf_dihedral_angle_d14.132307
X-RAY DIFFRACTIONf_chiral_restr0.068950
X-RAY DIFFRACTIONf_plane_restr0.0041083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9250.34061390.2982650X-RAY DIFFRACTION100
1.925-1.95140.30091380.2722626X-RAY DIFFRACTION100
1.9514-1.97930.29441380.25722620X-RAY DIFFRACTION100
1.9793-2.00880.23461380.24472624X-RAY DIFFRACTION100
2.0088-2.04020.28931400.22922644X-RAY DIFFRACTION100
2.0402-2.07360.231370.2052609X-RAY DIFFRACTION100
2.0736-2.10940.25131390.20612648X-RAY DIFFRACTION100
2.1094-2.14770.2371400.19062648X-RAY DIFFRACTION100
2.1477-2.18910.24431390.18832638X-RAY DIFFRACTION100
2.1891-2.23370.21821380.18492622X-RAY DIFFRACTION100
2.2337-2.28230.24681390.17972641X-RAY DIFFRACTION100
2.2823-2.33540.20151390.16752651X-RAY DIFFRACTION100
2.3354-2.39380.21831380.16792609X-RAY DIFFRACTION100
2.3938-2.45850.19161410.15762693X-RAY DIFFRACTION100
2.4585-2.53080.22351370.16062600X-RAY DIFFRACTION100
2.5308-2.61250.22461390.16222649X-RAY DIFFRACTION100
2.6125-2.70590.2131400.16352646X-RAY DIFFRACTION100
2.7059-2.81420.22181390.16632655X-RAY DIFFRACTION100
2.8142-2.94230.20981400.16672650X-RAY DIFFRACTION100
2.9423-3.09730.18831390.15962646X-RAY DIFFRACTION100
3.0973-3.29130.21541410.16212676X-RAY DIFFRACTION100
3.2913-3.54540.18871390.1552642X-RAY DIFFRACTION100
3.5454-3.90190.21410.15322669X-RAY DIFFRACTION100
3.9019-4.46610.14921410.13572686X-RAY DIFFRACTION100
4.4661-5.62490.18131410.15412687X-RAY DIFFRACTION100
5.6249-43.57080.18921460.19852752X-RAY DIFFRACTION100

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