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- PDB-6y4f: X-ray structure of the Zn-dependent receptor-binding domain of Pr... -

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Basic information

Entry
Database: PDB / ID: 6y4f
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 / adhesin
Function / homologyFimbrial-type adhesion domain superfamily / pilus / cell adhesion / metal ion binding / GLUTAMIC ACID / Fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7633
Polymers15,5501
Non-polymers2132
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6940 Å2
Unit cell
Length a, b, c (Å)26.655, 54.490, 79.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Fimbrial adhesin


Mass: 15550.442 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Gene: mrpH, PMI0270 / Production host: Escherichia coli BL21 (bacteria) / 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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus HT screen (Molecular Dimensions, UK) condition D9 (0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, ...Details: Morpheus HT screen (Molecular Dimensions, UK) condition D9 (0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M 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: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.75→19.05 Å / Num. obs: 12317 / % possible obs: 98.97 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.18 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Net I/σ(I): 12.7
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 7707 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.242 / Rrim(I) all: 0.614 / % possible all: 93.75

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
PHENIX1.18rc1_3777refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y4E

6y4e


Resolution: 1.75→19.05 Å / SU ML: 0.1464 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.0833
RfactorNum. reflection% reflection
Rfree0.1826 631 5.16 %
Rwork0.1527 --
obs0.1543 12225 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 11 183 1223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311106
X-RAY DIFFRACTIONf_angle_d0.70361517
X-RAY DIFFRACTIONf_chiral_restr0.0495166
X-RAY DIFFRACTIONf_plane_restr0.0043202
X-RAY DIFFRACTIONf_dihedral_angle_d12.6025416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.880.26841290.25142187X-RAY DIFFRACTION96.02
1.89-2.070.20231100.16482303X-RAY DIFFRACTION99.83
2.07-2.370.17171410.14472293X-RAY DIFFRACTION99.84
2.37-2.990.18311270.14252344X-RAY DIFFRACTION99.96
2.99-19.050.15481240.13562467X-RAY DIFFRACTION99.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4977444428410.159741376271-0.254917951460.895640774539-0.3726891002070.592147207283-0.04280126063020.0387259917727-0.0456316137597-0.06467027977510.03467335402050.03135715063640.0561146982889-0.02974290349190.01430662959430.0830062514159-0.00358931014436-0.007595110496020.0759701032122-0.006477495617090.086029513654-9.12006603004-1.6716653838715.7911271321
20.630428676793-0.06477018980880.3753589139310.791220214846-0.170613195251.474693795370.02488626701840.0530032339608-0.0633897644822-0.1197850729710.00616075164147-0.1397414649730.01963447149620.166667519915-0.01781829587850.0687775250956-0.007741714939250.01710402463050.09744224189050.0008485721191970.08333034830770.7008309158831.633168330196.81043096538
31.36707101916-0.526329867087-1.015342135520.9881923270640.4777431126442.12711670703-0.0688912947727-0.00684504631846-0.089821082770.0463167876964-0.0101183121648-0.05846569140230.147724007470.1255626563940.06715260616540.0978590089820.0175586004436-0.01048202075920.06832832719870.003664260096450.100052815589-4.76912341955-6.4605424524522.08380698
40.899625272710.0201003129633-0.211460136670.713711270709-0.370881569140.941904429366-0.01073180082090.01903453512920.0110955430639-0.06045241254660.014739467450.066206680460.0370454813048-0.0465869089689-0.01842107347640.0626240885520.00704408708682-0.005419638246910.06841124473910.005095794077310.0746106285275-11.9395917529-0.26383224151917.2917278426
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 84 )25 - 841 - 60
22chain 'A' and (resid 85 through 106 )85 - 10661 - 87
33chain 'A' and (resid 107 through 118 )107 - 11888 - 101
44chain 'A' and (resid 119 through 158 )119 - 158102 - 146

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