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- PDB-8tef: PorX primitive monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 8tef
TitlePorX primitive monoclinic crystal form
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 UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 6, 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
C: Response regulator receiver protein
D: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,24319
Polymers242,0894
Non-polymers1,15415
Water1,00956
1
A: Response regulator receiver protein
B: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,67010
Polymers121,0452
Non-polymers6258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-148 kcal/mol
Surface area40920 Å2
MethodPISA
2
C: Response regulator receiver protein
D: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5739
Polymers121,0452
Non-polymers5297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-134 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.520, 57.517, 149.141
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Response regulator receiver protein


Mass: 60522.262 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.2 M lithium sulfate, 0.1 M tris pH 8.1 and 35% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9823 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9823 Å / Relative weight: 1
ReflectionResolution: 2.85→46 Å / Num. obs: 53000 / % possible obs: 100 % / Redundancy: 4 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.058 / Rrim(I) all: 0.119 / Χ2: 0.926 / Net I/σ(I): 7.7 / Num. measured all: 210610
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.93.80.32525940.8910.9710.1910.3790.969100
2.9-2.953.90.29425840.9040.9740.1710.3420.954100
2.95-3.014.10.25726620.9390.9840.1420.2950.958100
3.01-3.074.10.24126210.940.9840.1350.2770.963100
3.07-3.144.10.21626280.9550.9890.120.2490.986100
3.14-3.214.10.19226510.9590.990.1070.2210.972100
3.21-3.294.10.16925780.9650.9910.0940.1940.957100
3.29-3.384.10.14726830.9740.9930.0830.170.997100
3.38-3.4840.13325810.9770.9940.0750.1540.979100
3.48-3.593.80.11526770.9780.9940.0670.1341.00699.9
3.59-3.723.80.10626060.9830.9960.0610.1221.03100
3.72-3.873.80.09226590.9860.9960.0540.1070.988100
3.87-4.044.20.08626410.9890.9970.0480.0990.938100
4.04-4.264.20.07726320.9910.9980.0420.0880.907100
4.26-4.524.10.06826740.9930.9980.0380.0780.96100
4.52-4.8740.06226520.9940.9980.0350.0710.852100
4.87-5.363.70.06326670.9920.9980.0370.0740.808100
5.36-6.143.90.0726830.9910.9980.0410.0820.781100
6.14-7.724.10.06427060.9940.9990.0360.0730.748100
7.72-463.70.04428210.9950.9990.0260.0520.773100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→45.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.551 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22159 2644 5 %RANDOM
Rwork0.17668 ---
obs0.17896 49956 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.17 Å2
2---1.01 Å2-0 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 2.85→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16780 0 59 56 16895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01217207
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616553
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.64123247
X-RAY DIFFRACTIONr_angle_other_deg0.4131.5738317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52652039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.036540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31103278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.22565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023738
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_it3.7064.8438162
X-RAY DIFFRACTIONr_mcbond_other3.7064.8438162
X-RAY DIFFRACTIONr_mcangle_it5.8598.71210190
X-RAY DIFFRACTIONr_mcangle_other5.8598.71210191
X-RAY DIFFRACTIONr_scbond_it4.3255.2769045
X-RAY DIFFRACTIONr_scbond_other4.35.2699002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9419.49312989
X-RAY DIFFRACTIONr_long_range_B_refined11.09459.1672016
X-RAY DIFFRACTIONr_long_range_B_other11.09459.1672015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.851→2.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 179 -
Rwork0.258 3266 -
obs--90.14 %

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