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- PDB-6tnj: Crystal structure of the vWF domain of the type V pili tip protei... -

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Basic information

Entry
Database: PDB / ID: 6tnj
TitleCrystal structure of the vWF domain of the type V pili tip protein Mfa5 from Porphyromonas gingivalis
ComponentsMinor fimbrium subunit Mfa5
KeywordsCELL ADHESION / Intramolekular Isopeptide / von Willebrand factor / Bacterial adhesion / Phorphyromonas gingivalis / Mfa1 fimbriae / Type V pili
Function / homologyvon Willebrand factor type A domain / pilus / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Minor fimbrium subunit Mfa5
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHeidler, T.V. / Claesson, R. / Persson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Other privateKempe Foundation Sweden
Citation
Journal: Commun Biol / Year: 2021
Title: Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.
Authors: Heidler, T.V. / Ernits, K. / Ziolkowska, A. / Claesson, R. / Persson, K.
#1: Journal: Commun Biol / Year: 2021
Title: Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.
Authors: Heidler, T.V. / Ernits, K. / Ziolkowska, A. / Claesson, R. / Persson, K.
History
DepositionDec 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / reflns / software / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value ..._pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.B_iso_Wilson_estimate / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Missing anisotropic B-factor
Details: Initial uploaded structure had b-factors of 0 at CE BMET A250 and associated hydrogens.
Provider: author / Type: Coordinate replacement
Revision 2.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Minor fimbrium subunit Mfa5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0254
Polymers32,7361
Non-polymers2893
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-21 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.198, 110.080, 38.178
Angle α, β, γ (deg.)90.000, 98.109, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Minor fimbrium subunit Mfa5


Mass: 32735.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0291 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG5
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG500, 10% PEG 20k, 0.1M Sodium Hepes / MOPS pH7.5, 0.1M Glu/Ala/Gly/Lys/Ser

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.54003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54003 Å / Relative weight: 1
ReflectionResolution: 1.85→37.85 Å / Num. obs: 23968 / % possible obs: 97.6 % / Redundancy: 171.8 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.087 / Net I/σ(I): 75.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 109.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 24 / Num. unique obs: 1123 / CC1/2: 0.995 / Rrim(I) all: 0.373 / % possible all: 75.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→37.8 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.8428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 2013 8.41 %
Rwork0.1317 21920 -
obs0.1356 23933 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 15 389 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842419
X-RAY DIFFRACTIONf_angle_d1.0293308
X-RAY DIFFRACTIONf_chiral_restr0.0549372
X-RAY DIFFRACTIONf_plane_restr0.0071437
X-RAY DIFFRACTIONf_dihedral_angle_d17.4987345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.21641210.2131183X-RAY DIFFRACTION76.44
1.9-1.950.24891320.16361436X-RAY DIFFRACTION89.55
1.95-20.19051330.13181629X-RAY DIFFRACTION99.72
2-2.070.18721570.12421586X-RAY DIFFRACTION100
2.07-2.140.191340.11971612X-RAY DIFFRACTION99.89
2.14-2.230.1791580.11951594X-RAY DIFFRACTION100
2.23-2.330.16851470.11461605X-RAY DIFFRACTION100
2.33-2.450.1911400.11671584X-RAY DIFFRACTION99.94
2.45-2.610.16751510.11991602X-RAY DIFFRACTION100
2.61-2.810.18681520.13161610X-RAY DIFFRACTION99.94
2.81-3.090.18421480.1391603X-RAY DIFFRACTION99.89
3.09-3.540.18711440.13741640X-RAY DIFFRACTION99.89
3.54-4.450.13841470.12211606X-RAY DIFFRACTION99.89
4.46-37.80.16231490.14731630X-RAY DIFFRACTION99.89

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