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- PDB-8thp: PorX phosphatase null mutant (T271V) -

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Basic information

Entry
Database: PDB / ID: 8thp
TitlePorX phosphatase null mutant (T271V)
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 / PglZ 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
Response regulator receiver protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 17, 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)121,2937
Polymers121,0412
Non-polymers2525
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-77 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.089, 96.978, 130.940
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: 60520.293 Da / Num. of mol.: 2 / Mutation: T271V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101
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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.14
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.14, 14.4% polyethylene glycol 8K, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 34201 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.047 / Rrim(I) all: 0.108 / Χ2: 1.415 / Net I/σ(I): 7.6 / Num. measured all: 169922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.10.36716560.8650.9630.1790.4090.60699.8
2.64-2.695.10.35917030.8650.9630.1730.40.665100
2.69-2.7450.31416740.8850.9690.1540.3510.7399.8
2.74-2.84.70.27916840.9050.9750.140.3130.81699.9
2.8-2.8650.25416810.9180.9780.1240.2830.87299.8
2.86-2.935.40.24516890.9440.9850.1140.2710.976100
2.93-35.40.22316790.9540.9880.1040.2460.976100
3-3.085.40.19417080.9590.9890.090.2141.187100
3.08-3.175.30.17417020.970.9920.0810.1921.286100
3.17-3.285.30.15616930.9720.9930.0750.1741.406100
3.28-3.395.20.13716890.9820.9960.0650.1521.542100
3.39-3.535.10.12616980.9870.9970.060.141.807100
3.53-3.695.10.10816980.9890.9970.0520.121.982100
3.69-3.884.90.09717230.9870.9970.0480.1092.057100
3.88-4.134.80.08717000.9910.9980.0430.0972.09299.9
4.13-4.454.50.07217290.9920.9980.0380.0822.20699.9
4.45-4.8940.06117290.9940.9980.0340.072.06599.9
4.89-5.64.30.06417400.9940.9980.0330.0721.91299.5
5.6-7.054.80.06217570.9960.9990.030.0691.81299.2
7.05-504.80.03718690.99910.0170.0411.65599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.95 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.848 / SU B: 19.614 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30458 1800 5.3 %RANDOM
Rwork0.24968 ---
obs0.25256 32346 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.536 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å2-0 Å20 Å2
2---1.09 Å20 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 2.6→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8257 0 10 44 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168144
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.64111395
X-RAY DIFFRACTIONr_angle_other_deg0.3621.57118843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.569520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.146101607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021842
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_it4.6815.0524009
X-RAY DIFFRACTIONr_mcbond_other4.6815.0524009
X-RAY DIFFRACTIONr_mcangle_it7.2379.0814999
X-RAY DIFFRACTIONr_mcangle_other7.2369.0815000
X-RAY DIFFRACTIONr_scbond_it4.295.3174434
X-RAY DIFFRACTIONr_scbond_other4.295.3174435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8669.6726396
X-RAY DIFFRACTIONr_long_range_B_refined12.44861.2336682
X-RAY DIFFRACTIONr_long_range_B_other12.44861.2336683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 120 -
Rwork0.355 2288 -
obs--96.86 %

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