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- PDB-8tfm: PorX with Zn (primitive orthorhombic crystal form) -

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Basic information

Entry
Database: PDB / ID: 8tfm
TitlePorX with Zn (primitive orthorhombic 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 / 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
Response regulator receiver protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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)121,62110
Polymers121,0452
Non-polymers5778
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-172 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.868, 97.058, 132.037
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
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, 25% glycerol and 0.2 mM Zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.283 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 31924 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.033 / Rrim(I) all: 0.118 / Χ2: 0.71 / Net I/σ(I): 5.4 / Num. measured all: 404150
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.72-2.7710.50.82915120.9010.9740.2570.870.37497.7
2.77-2.8211.70.72515640.9480.9870.2140.7570.37999.1
2.82-2.8712.60.68715630.9510.9870.1950.7150.3999.9
2.87-2.9313.30.61115760.9680.9920.1710.6350.39100
2.93-2.9913.50.53815770.9750.9940.150.5590.409100
2.99-3.0613.60.48215770.9780.9940.1340.5010.415100
3.06-3.1413.60.36615670.9860.9960.1020.380.445100
3.14-3.2213.60.32515880.990.9970.0910.3380.476100
3.22-3.3213.40.26215810.9920.9980.0730.2720.514100
3.32-3.4313.40.2115880.9950.9990.0590.2190.571100
3.43-3.5513.40.17815850.9960.9990.050.1850.601100
3.55-3.6913.20.14615940.9970.9990.0410.1520.701100
3.69-3.86130.12115860.9970.9990.0350.1260.788100
3.86-4.0612.50.10315950.9970.9990.030.1080.859100
4.06-4.3211.60.08716060.99810.0270.0920.997100
4.32-4.6510.90.07316120.99810.0230.0771.173100
4.65-5.12120.06916090.99810.0210.0721.187100
5.12-5.8611.60.06816310.9980.9990.0210.0711.071100
5.86-7.3813.40.06316600.99910.0180.0661.068100
7.38-5012.50.0417530.99910.0120.0421.4299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→48.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 38.444 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26111 1593 5 %RANDOM
Rwork0.20431 ---
obs0.20717 30273 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.039 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å2-0 Å20 Å2
2--0.67 Å2-0 Å2
3----4.32 Å2
Refinement stepCycle: 1 / Resolution: 2.72→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8273 0 18 26 8317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128450
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168140
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.64111408
X-RAY DIFFRACTIONr_angle_other_deg0.4381.5718833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1151001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.563519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.902101600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021839
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_it3.4574.0854019
X-RAY DIFFRACTIONr_mcbond_other3.4574.0854019
X-RAY DIFFRACTIONr_mcangle_it5.4477.3415015
X-RAY DIFFRACTIONr_mcangle_other5.4477.3415016
X-RAY DIFFRACTIONr_scbond_it3.7154.4054431
X-RAY DIFFRACTIONr_scbond_other3.7154.4064432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0437.9626394
X-RAY DIFFRACTIONr_long_range_B_refined10.19149.3135662
X-RAY DIFFRACTIONr_long_range_B_other10.19149.3235663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.736 Å
RfactorNum. reflection% reflection
Rfree0.366 90 -
Rwork0.308 1640 -
obs--73.12 %
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)
10.2284-0.2942-0.2840.44850.65431.6706-0.0491-0.1212-0.1639-0.02390.27030.137-0.09010.6558-0.22120.3997-0.0948-0.05790.2684-0.05140.3012-19.4509-1.5885-29.9349
20.1334-0.3142-0.32681.28360.55150.9003-0.05830.02680.01320.30150.043-0.09930.0169-0.10030.01530.4719-0.0245-0.05230.0302-0.00570.1981-40.64756.5312-19.6306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 517
2X-RAY DIFFRACTION2B2 - 517

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