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- PDB-6y4e: X-ray structure of the Zn-dependent receptor-binding domain of Pr... -

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Basic information

Entry
Database: PDB / ID: 6y4e
TitleX-ray structure of the Zn-dependent receptor-binding domain of Proteus mirabilis MR/P fimbrial adhesin MrpH
ComponentsFimbrial adhesin
KeywordsCELL ADHESION / Metal binding protein / fimbrial adhesin
Function / homologyFimbrial-type adhesion domain superfamily / pilus / cell adhesion / metal ion binding / L(+)-TARTARIC ACID / Fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.02 Å
AuthorsKnight, S.D. / Ubhayasekera, W. / Jiang, W.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2016-04451 Sweden
CitationJournal: Plos Pathog. / Year: 2020
Title: MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation.
Authors: Jiang, W. / Ubhayasekera, W. / Breed, M.C. / Norsworthy, A.N. / Serr, N. / Mobley, H.L.T. / Pearson, M.M. / Knight, S.D.
History
DepositionFeb 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2623
Polymers15,0471
Non-polymers2152
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-38 kcal/mol
Surface area6970 Å2
Unit cell
Length a, b, c (Å)25.561, 53.139, 40.158
Angle α, β, γ (deg.)90.000, 102.835, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fimbrial adhesin


Mass: 15046.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Gene: mrpH, PMI0270 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EUK6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.77 Å3/Da / Density % sol: 30.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus HT screen (Molecular Dimensions, UK) condition C9 (0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic and 0.03 M ammonium sulfate, 0.1 bicine/Trizma base pH 8.5, 10% w/v PEG ...Details: Morpheus HT screen (Molecular Dimensions, UK) condition C9 (0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic and 0.03 M ammonium sulfate, 0.1 bicine/Trizma base pH 8.5, 10% w/v PEG 20000 and 20% v/v PEG MME 550).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.02→39.15 Å / Num. obs: 52285 / % possible obs: 98.22 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.17 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0461 / Rpim(I) all: 0.0227 / Rrim(I) all: 0.0516 / Net I/σ(I): 15
Reflection shellResolution: 1.02→1.056 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 20712 / CC1/2: 0.878 / CC star: 0.967 / Rpim(I) all: 0.3 / Rrim(I) all: 0.629 / % possible all: 95.05

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
PHENIX1.18rc1_3777refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.02→39.15 Å / SU ML: 0.0612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.8279
RfactorNum. reflection% reflection
Rfree0.1282 2563 4.9 %
Rwork0.1071 --
obs0.1081 52268 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.54 Å2
Refinement stepCycle: LAST / Resolution: 1.02→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 11 161 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951176
X-RAY DIFFRACTIONf_angle_d1.07751631
X-RAY DIFFRACTIONf_chiral_restr0.0828180
X-RAY DIFFRACTIONf_plane_restr0.0075220
X-RAY DIFFRACTIONf_dihedral_angle_d14.246440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.040.25511070.22112677X-RAY DIFFRACTION95.02
1.04-1.060.22141370.19362664X-RAY DIFFRACTION94.95
1.06-1.080.17371440.16022661X-RAY DIFFRACTION95.96
1.08-1.110.16691430.13812737X-RAY DIFFRACTION97.1
1.11-1.140.14491480.12122700X-RAY DIFFRACTION97.27
1.14-1.170.11891420.10742740X-RAY DIFFRACTION97.83
1.17-1.20.11691320.12758X-RAY DIFFRACTION98.4
1.2-1.240.12971600.09482763X-RAY DIFFRACTION99.08
1.24-1.290.1291440.08792816X-RAY DIFFRACTION99.03
1.29-1.340.11771270.08932802X-RAY DIFFRACTION99.15
1.34-1.40.11751410.08662742X-RAY DIFFRACTION98.8
1.4-1.470.10991720.08332773X-RAY DIFFRACTION99.53
1.47-1.560.1131470.08132787X-RAY DIFFRACTION99.42
1.56-1.680.10961510.08282812X-RAY DIFFRACTION99.5
1.68-1.850.12181320.0922803X-RAY DIFFRACTION99.06
1.85-2.120.11711720.0942793X-RAY DIFFRACTION99.33
2.12-2.670.10591260.10672822X-RAY DIFFRACTION99.49
2.67-39.150.14841380.12332855X-RAY DIFFRACTION99.04

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