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- PDB-1o75: Tp47, the 47-Kilodalton Lipoprotein of Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 1o75
TitleTp47, the 47-Kilodalton Lipoprotein of Treponema pallidum
Components47 KDA MEMBRANE ANTIGEN
KeywordsLIPOPROTEINULLNTIGEN / PENICILLIN-BINDING PROTEIN / INTEGRAL MEMBRANE LIPOPROTEIN / IMMUNOGEN / FOUR-DOMAIN PROTEIN / ANTIGEN / LIPOPROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / plasma membrane
Similarity search - Function
Penicillin-binding protein Tp47, domain B / Penicillin-binding protein Tp47, domain D / Penicillin-binding protein Tp47, domain C / Penicillin-binding protein Tp47, domain A / Penicillin-binding protein Tp47, domain C / Penicillin-binding protein Tp47, domain D / Penicillin-binding protein Tp47 domain A / Tp47, N-terminal domain superfamily / Tp47 lipoprotein, middle and C-terminal domain / Tp47, domain C superfamily ...Penicillin-binding protein Tp47, domain B / Penicillin-binding protein Tp47, domain D / Penicillin-binding protein Tp47, domain C / Penicillin-binding protein Tp47, domain A / Penicillin-binding protein Tp47, domain C / Penicillin-binding protein Tp47, domain D / Penicillin-binding protein Tp47 domain A / Tp47, N-terminal domain superfamily / Tp47 lipoprotein, middle and C-terminal domain / Tp47, domain C superfamily / Penicillin-binding protein Tp47 domain C / Penicillin-binding protein Tp47 domain a / Dna Ligase; domain 1 / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
XENON / Putative DD-carboxypeptidase TP_0574
Similarity search - Component
Biological speciesTREPONEMA PALLIDUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsDeka, R.K. / Machius, M. / Norgard, M.V. / Tomchick, D.R.
Citation
Journal: J. Biol. Chem. / Year: 2002
Title: Crystal structure of the 47-kDa lipoprotein of Treponema pallidum reveals a novel penicillin-binding protein.
Authors: Deka, R.K. / Machius, M. / Norgard, M.V. / Tomchick, D.R.
#1: Journal: Proc.Natl.Acad.Sci. USA / Year: 1994
Title: The 47-kDa Major Lipoprotein Immunogen of Treponema Pallidum is a Penicillin-Binding Protein with Carboxypeptidase Activity
Authors: Weigel, L.M. / Radolf, J.D. / Norgard, M.V.
History
DepositionOct 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 47 KDA MEMBRANE ANTIGEN
B: 47 KDA MEMBRANE ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6488
Polymers91,3292
Non-polymers1,3196
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.931, 128.931, 151.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE OLIGOMERIZATION STATE OF THE PROTEIN IN SOLUTIONIS MONOMERIC, AS DETERMINED VIA ANALYTICALULTRACENTRIFUGATION. THE BIOLOGICALLY SIGNIFICANTOLIGOMERIZATION STATE OF THE MEMBRANCE BOUNDLIPOPROTIEN IS UNKNOWN

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Components

#1: Protein 47 KDA MEMBRANE ANTIGEN


Mass: 45664.566 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TREPONEMA PALLIDUM (bacteria) / Plasmid: PASK-IBA7 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P29723
#2: Polysaccharide 2,3-di-O-sulfo-alpha-D-glucopyranose-(1-6)-2,3-di-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 662.549 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcp[2S,3S]a1-6DGlcp[2S,3S]a1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp2SO33SO3]{[(6+1)][a-D-Glcp2SO33SO3]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Xe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS MEMBRANE LIPOPROTEIN IS A PATHOGEN-SPECIFIC MEMBRANE IMMUNOGEN FOUND ONLY IN TREPONEMES. MAY ...THIS MEMBRANE LIPOPROTEIN IS A PATHOGEN-SPECIFIC MEMBRANE IMMUNOGEN FOUND ONLY IN TREPONEMES. MAY PLAY AN IMPORTANT ROLE IN THE CELL ENVELOPE OF VIRULENT TREPONEMA. ENGINEERED MUTATION HIS 24 SER AND HIS 28 SER, CHAINS A, B
Sequence detailsTHE FIRST 20 RESIDUES OF THIS SEQUENCE ENCODES FOR THE LIPIDATED MEMBRANE ANCHOR. THE POST- ...THE FIRST 20 RESIDUES OF THIS SEQUENCE ENCODES FOR THE LIPIDATED MEMBRANE ANCHOR. THE POST-TRANSLATIONALLY MODIFIED N-TERMINAL CYSTEINE OF NATIVE TP47 WAS DESIGNATED AS AMINO ACID #1. ONLY RESIDUES 2-415 WERE EXPRESSED.

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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: 3.97 Å3/Da / Density % sol: 45 %
Crystal growpH: 5.6
Details: 32% PEG 4000, 100 MM SODIUM CITRATE PH 5.6, 200 MM AMMONIUM ACETATE,3% (W/V) DEXTRAN SULFATE 8000
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMHEPES1droppH7.4
320 mM1dropNaCl
432 %(w/v)PEG40001reservoir
5100 mMsodium citrate1reservoirpH5.6
6200 mMammonium acetate1reservoir
73 %(w/v)dextran sulfate 80001reservoir
80.100 mM1reservoirplus or minusZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97938
DetectorType: APS SBC2 / Detector: CCD / Date: Feb 1, 2001 / Details: DUAL SLITS
RadiationMonochromator: GRAPHITE DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.95→28.2 Å / Num. obs: 478972 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.9 / % possible all: 100
Reflection
*PLUS
Num. obs: 105601 / Num. measured all: 478972
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→28.2 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3136619.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5036 5.1 %RANDOM
Rwork0.205 ---
obs0.205 101021 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.91 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 44 619 6900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 409 4.7 %
Rwork0.291 8287 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMLIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARION.TOP
Refinement
*PLUS
Lowest resolution: 35 Å / Num. reflection obs: 94665 / Num. reflection Rfree: 6356
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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