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- PDB-8ted: PorX primitive orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 8ted
TitlePorX 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
ACETATE ION / BROMIDE ION / Response regulator receiver protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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

Downloads & links

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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)123,18232
Polymers121,0452
Non-polymers2,13730
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-78 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.696, 97.849, 133.200
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)
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
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 and 20% glycerol, 0.5 M sodium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→46.16 Å / Num. obs: 65014 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 0.99 / Net I/σ(I): 13.7 / Num. measured all: 434300
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.573 / Num. measured all: 31100 / Num. unique obs: 4531 / CC1/2: 0.925 / Rpim(I) all: 0.234 / Rrim(I) all: 0.62 / Χ2: 1 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→42.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.216 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22563 3297 5.1 %RANDOM
Rwork0.17863 ---
obs0.181 61660 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.631 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---0.85 Å20 Å2
3---2.76 Å2
Refinement stepCycle: 1 / Resolution: 2.1→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 33 686 9105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168360
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.64111724
X-RAY DIFFRACTIONr_angle_other_deg1.2721.58219364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88651037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45525.046434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.452151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2381520
X-RAY DIFFRACTIONr_chiral_restr0.0720.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021891
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_it2.4823.0744119
X-RAY DIFFRACTIONr_mcbond_other2.4783.0744117
X-RAY DIFFRACTIONr_mcangle_it3.6114.5995147
X-RAY DIFFRACTIONr_mcangle_other3.614.65148
X-RAY DIFFRACTIONr_scbond_it3.1823.454556
X-RAY DIFFRACTIONr_scbond_other3.1823.454557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9275.0226572
X-RAY DIFFRACTIONr_long_range_B_refined7.18958.28936779
X-RAY DIFFRACTIONr_long_range_B_other7.12658.15836225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16391 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 224 -
Rwork0.268 4544 -
obs--99.02 %

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