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- PDB-5jir: Crystal structure of Treponema pallidum protein Tp0624 -

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Basic information

Entry
Database: PDB / ID: 5jir
TitleCrystal structure of Treponema pallidum protein Tp0624
ComponentsOOP family OmpA-OmpF porin
KeywordsUNKNOWN FUNCTION / OmpA-like / peptidoglycan / modular assembly / neofunctionalized
Function / homologyOmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / membrane / Uncharacterized protein
Function and homology information
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsParker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Plos One / Year: 2016
Title: The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains.
Authors: Parker, M.L. / Houston, S. / Wetherell, C. / Cameron, C.E. / Boulanger, M.J.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: OOP family OmpA-OmpF porin
A: OOP family OmpA-OmpF porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,13514
Polymers93,4832
Non-polymers65212
Water6,233346
1
B: OOP family OmpA-OmpF porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0117
Polymers46,7411
Non-polymers2696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: OOP family OmpA-OmpF porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1247
Polymers46,7411
Non-polymers3836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-99 kcal/mol
Surface area36120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.020, 103.500, 140.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OOP family OmpA-OmpF porin / Uncharacterized protein


Mass: 46741.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (strain Nichols) (bacteria)
Strain: Nichols / Gene: TP_0624, TPANIC_0624 / Production host: Escherichia coli (E. coli) / References: UniProt: O83632
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 M Hepes pH 6.8, 0.25 M MgCl2, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: ACCEL/BRUKER double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→63.02 Å / Num. obs: 101666 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimlessdata scaling
SHELXphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→51.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 5075 5 %Random selection
Rwork0.1891 ---
obs0.1903 101597 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 28.1832 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.7→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 0 32 346 6793
Biso mean--31.29 29.11 -
Num. residues----818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086587
X-RAY DIFFRACTIONf_angle_d1.18950
X-RAY DIFFRACTIONf_chiral_restr0.0431032
X-RAY DIFFRACTIONf_plane_restr0.0051155
X-RAY DIFFRACTIONf_dihedral_angle_d13.2122457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71940.26481640.251931713335100
1.7194-1.73960.2911420.245832043346100
1.7396-1.76080.24921750.237431873362100
1.7608-1.78310.28231620.226232123374100
1.7831-1.80650.27191830.224231453328100
1.8065-1.83130.26191580.216832003358100
1.8313-1.85750.26021840.207332273411100
1.8575-1.88520.22151730.207631283301100
1.8852-1.91460.25751700.20232123382100
1.9146-1.9460.25061620.203531813343100
1.946-1.97960.22981630.201632093372100
1.9796-2.01560.24881720.198531993371100
2.0156-2.05440.18861730.197531873360100
2.0544-2.09630.26231570.193832073364100
2.0963-2.14190.21211890.192131823371100
2.1419-2.19170.23781720.19731843356100
2.1917-2.24650.22851670.184632243391100
2.2465-2.30730.2261920.185831763368100
2.3073-2.37520.22761730.179332213394100
2.3752-2.45180.22211580.188532193377100
2.4518-2.53940.20771720.188832213393100
2.5394-2.64110.2241720.193332143386100
2.6411-2.76130.23231700.196932373407100
2.7613-2.90690.22471670.198132453412100
2.9069-3.0890.22751710.193632373408100
3.089-3.32740.20561650.194132773442100
3.3274-3.66220.19771670.180232603427100
3.6622-4.19190.17321900.160432903480100
4.1919-5.28060.16761570.15833393496100
5.2806-51.7740.21641550.20163327348295

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