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- PDB-1xs5: The Crystal Structure of Lipoprotein Tp32 from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 1xs5
TitleThe Crystal Structure of Lipoprotein Tp32 from Treponema pallidum
ComponentsMembrane lipoprotein TpN32
KeywordsMEMBRANE PROTEIN / lipoprotein / periplasmic binding protein / methionine
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / Membrane lipoprotein TpN32
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsDeka, R.K. / Neil, L. / Hagman, K.E. / Machius, M. / Tomchick, D.R. / Brautigam, C.A. / Norgard, M.V.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural evidence that the 32-kilodalton lipoprotein (Tp32) of Treponema pallidum is an L-methionine-binding protein
Authors: Deka, R.K. / Neil, L. / Hagman, K.E. / Machius, M. / Tomchick, D.R. / Brautigam, C.A. / Norgard, M.V.
History
DepositionOct 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane lipoprotein TpN32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6372
Polymers26,4881
Non-polymers1491
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.248, 46.404, 55.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsMonomer contained in asymmetric unit is the biological unit.

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Components

#1: Protein Membrane lipoprotein TpN32 / 29 kDa protein


Mass: 26488.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tpn32 / Plasmid: pProEX HTb-Tp32 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: O07950
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.245 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: succinic acid, pH 7.0, 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: 0.98 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 23, 2003
RadiationMonochromator: Double-crystal monochromator, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→35.5 Å / Num. all: 21397 / Num. obs: 21397 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 907 / Rsym value: 0.587 / % possible all: 87.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 594357.42 / 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
Rfree0.232 1417 7 %RANDOM
Rwork0.183 ---
all0.186 20386 --
obs0.183 20386 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9267 Å2 / ksol: 0.32875 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20 Å20 Å2
2--6.73 Å20 Å2
3----3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.85→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 9 202 2092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 183 6.6 %
Rwork0.263 2585 -
obs-2585 78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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