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- PDB-2o6c: Structure of selenomethionyl rTp34 from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 2o6c
TitleStructure of selenomethionyl rTp34 from Treponema pallidum
Components34 kDa membrane antigen
KeywordsMEMBRANE PROTEIN / PROTEIN BINDING / Ig-fold / syphilis / metal-ion binding / dimer
Function / homology
Function and homology information


Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
34 kDa membrane antigen
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMachius, M. / Brautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Lumpkins, S.B. / Norgard, M.V.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin.
Authors: Deka, R.K. / Brautigam, C.A. / Tomson, F.L. / Lumpkins, S.B. / Tomchick, D.R. / Machius, M. / Norgard, M.V.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 34 kDa membrane antigen
B: 34 kDa membrane antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,90810
Polymers41,4502
Non-polymers4588
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-76 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.410, 66.020, 150.992
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 34 kDa membrane antigen / Pathogen-specific membrane antigen


Mass: 20724.820 Da / Num. of mol.: 2 / Mutation: V16G, F17A, S18M, A19G, C20S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tpd / Plasmid: pProExHTa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P19478
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, 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: 0.97943 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 22, 2004
RadiationMonochromator: Double-crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.7→23.53 Å / Num. all: 38808 / Num. obs: 38808 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.076 / Net I/σ(I): 39.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3284 / Rsym value: 0.782 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→23.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.089 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3863 10 %RANDOM
Rwork0.184 ---
obs0.187 38740 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.414 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---1.07 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 22 221 2728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212632
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9343583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92824.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.402158
X-RAY DIFFRACTIONr_chiral_restr0.1390.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022445
X-RAY DIFFRACTIONr_nbd_refined0.1890.21110
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.28
X-RAY DIFFRACTIONr_mcbond_it1.3021.51622
X-RAY DIFFRACTIONr_mcangle_it1.78822555
X-RAY DIFFRACTIONr_scbond_it2.79131153
X-RAY DIFFRACTIONr_scangle_it4.4164.51028
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 275 -
Rwork0.305 2344 -
obs-2619 93.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44970.32410.78531.28750.82141.591-0.0099-0.03390.0082-0.1420.04360.0097-0.02090.0189-0.0337-0.09410.0047-0.0077-0.0057-0.0419-0.027310.889241.304161.4519
20.76330.85340.83361.86781.76911.67730.219-0.1041-0.12840.2225-0.0041-0.10670.3619-0.0805-0.21490.0825-0.0219-0.1119-0.08810.0028-0.05826.43914.896952.3489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA28 - 18532 - 189
22BB29 - 18533 - 189

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