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- PDB-2fqy: PnrA from Treponema pallidum complexed with adenosine. -

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Basic information

Entry
Database: PDB / ID: 2fqy
TitlePnrA from Treponema pallidum complexed with adenosine.
ComponentsMembrane lipoprotein tmpC
KeywordsTRANSPORT PROTEIN / ABC receptor protein / nucleoside binding protein
Function / homology
Function and homology information


: / ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / Membrane lipoprotein TmpC
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Machius, M. / Norgard, M.V.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum
Authors: Deka, R.K. / Brautigam, C.A. / Yang, X.F. / Blevins, J.S. / Machius, M. / Tomchick, D.R. / Norgard, M.V.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane lipoprotein tmpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3262
Polymers34,0591
Non-polymers2671
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.620, 69.097, 69.656
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 Membrane lipoprotein tmpC / Membrane protein C / 35 kDa antigen / Lipoprotein TpN35 / Tp0319 / TmpC / PnrA


Mass: 34058.504 Da / Num. of mol.: 1 / Fragment: soluble portion of PnrA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tmpC / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P29724
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% (w/v) PEG 4000., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. all: 21309 / Num. obs: 21309 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3 / Num. unique all: 1842 / % possible all: 86.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PnrA that was solved with inosine, inosine omitted

Resolution: 1.9→49 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1634357.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 612 2.9 %RANDOM
Rwork0.187 ---
all0.188 21272 --
obs0.187 21272 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1101 Å2 / ksol: 0.368206 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å20 Å2
2---5.12 Å20 Å2
3---10.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 19 171 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it2.091.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it3.232
X-RAY DIFFRACTIONc_scangle_it4.642.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 86 2.7 %
Rwork0.26 3066 -
obs-3066 88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.param

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