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- PDB-8tff: PorX with BeF3 phosphate analog -

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Basic information

Entry
Database: PDB / ID: 8tff
TitlePorX with BeF3 phosphate analog
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / Type-IX secretion system / response regulator / alkaline phosphatase
Function / homology
Function and homology information


phosphorelay signal transduction system / metal ion binding
Similarity search - Function
PglZ domain / BREX system PglZ alkaline phosphatase-like domain / : / Alkaline-phosphatase-like, core domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
ACETATE ION / BERYLLIUM TRIFLUORIDE ION / Response regulator receiver protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsSaran, A. / Zeytuni, N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Pnas Nexus / Year: 2024
Title: Unveiling the molecular mechanisms of the type IX secretion system's response regulator: Structural and functional insights.
Authors: Saran, A. / Kim, H.M. / Manning, I. / Hancock, M.A. / Schmitz, C. / Madej, M. / Potempa, J. / Sola, M. / Trempe, J.F. / Zhu, Y. / Davey, M.E. / Zeytuni, N.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver protein
B: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64814
Polymers121,0452
Non-polymers60412
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-77 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.320, 97.518, 131.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Response regulator receiver protein


Mass: 60522.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae UW101 (bacteria)
Gene: Fjoh_2906 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5FFU4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4% polyethylene glycol 8000, 20% glycerol, 0.166 mM beryllium sulphate, 1.162 mM Sodium fluoride and 0.083 mM Manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 46485 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Χ2: 0.861 / Net I/σ(I): 5.5 / Num. measured all: 304993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.34-2.386.30.42222860.9180.9780.1820.460.567100
2.38-2.426.70.39822780.9270.9810.1650.4310.567100
2.42-2.476.80.36722850.9480.9870.150.3960.587100
2.47-2.526.80.33923090.9550.9880.140.3670.651100
2.52-2.586.70.30622810.9640.9910.1280.3320.615100
2.58-2.646.60.28923220.9580.9890.1210.3130.605100
2.64-2.76.30.25722720.9650.9910.1110.280.671100
2.7-2.776.60.22822940.9760.9940.0960.2470.661100
2.77-2.866.70.20322960.9780.9940.0840.220.72899.9
2.86-2.956.40.17923100.9820.9950.0770.1950.743100
2.95-3.056.80.15923150.9880.9970.0650.1720.804100
3.05-3.186.90.13923060.9870.9970.0570.150.888100
3.18-3.326.70.12123130.9910.9980.0510.1310.955100
3.32-3.56.30.10523210.9910.9980.0450.1141.102100
3.5-3.716.60.09923270.9930.9980.0420.1081.37100
3.71-46.40.08523390.9930.9980.0370.0931.26100
4-4.46.80.07223300.9950.9990.030.0781.259100
4.4-5.046.40.06223760.9960.9990.0270.0681.19100
5.04-6.356.40.06423970.9960.9990.0270.0690.908100
6.35-506.20.05425280.9960.9990.0240.0591.058100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→48.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.853 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23098 2363 5.1 %RANDOM
Rwork0.1651 ---
obs0.16842 44058 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.766 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---1.67 Å20 Å2
3---3.87 Å2
Refinement stepCycle: 1 / Resolution: 2.34→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8431 0 27 381 8839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128667
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168331
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.64411706
X-RAY DIFFRACTIONr_angle_other_deg0.4561.57119291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12751034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.449520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.579101651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021886
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5093.5464113
X-RAY DIFFRACTIONr_mcbond_other3.5043.5454112
X-RAY DIFFRACTIONr_mcangle_it5.2746.3555136
X-RAY DIFFRACTIONr_mcangle_other5.2746.3555137
X-RAY DIFFRACTIONr_scbond_it4.2733.9994554
X-RAY DIFFRACTIONr_scbond_other4.2713.9974543
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6737.1196553
X-RAY DIFFRACTIONr_long_range_B_refined9.44942.7237127
X-RAY DIFFRACTIONr_long_range_B_other9.45142.7237087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.398 Å
RfactorNum. reflection% reflection
Rfree0.222 184 -
Rwork0.202 3101 -
obs--97.3 %

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