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- PDB-2v84: Crystal Structure of the Tp0655 (TpPotD) Lipoprotein of Treponema... -

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Basic information

Entry
Database: PDB / ID: 2v84
TitleCrystal Structure of the Tp0655 (TpPotD) Lipoprotein of Treponema pallidum
ComponentsSPERMIDINE/PUTRESCINE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER / POLYAMINE BINDING / TREPONEMA PALLIDUM / SYPHILIS / SPERMIDINE / PUTRESCINE / LIPOPROTEIN
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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
Spermidine/putrescine ABC transporter, periplasmic binding protein (PotD)
Similarity search - Component
Biological speciesTREPONEMA PALLIDUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsMachius, M. / Brautigam, C.A. / Tomchick, D.R. / Ward, P. / Otwinowski, Z. / Blevine, J.S. / Deka, R.K. / Norgard, M.V.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and Biochemical Basis for Polyamine Binding to the Tp0655 Lipoprotein of Treponema Pallidum: Putative Role for Tp0655 (Tppotd) as a Polyamine Receptor.
Authors: Machius, M. / Brautigam, C.A. / Tomchick, D.R. / Ward, P. / Otwinowski, Z. / Blevins, J.S. / Deka, R.K. / Norgard, M.V.
History
DepositionAug 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPERMIDINE/PUTRESCINE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7118
Polymers39,1431
Non-polymers5687
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.610, 86.270, 89.500
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 SPERMIDINE/PUTRESCINE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN / TP0655 LIPOPROTEIN / POTD


Mass: 39143.047 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-348
Source method: isolated from a genetically manipulated source
Details: CONSTRUCT USED LACKS THE FIRST AMINO ACID RESIDUE (I.E. CYSTEINE) WHICH IS POST-TRANSLATIONALLY ACYLATED.
Source: (gene. exp.) TREPONEMA PALLIDUM (bacteria) / Strain: NICHOLS
Description: NICHOLS STRAIN ISOLATED FROM CEREBROSPINAL FLUID OF A NEUROSYPHILIS PATIENT
Plasmid: PIVEX2.4D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-AI / References: UniProt: O83661
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.5 Å3/Da / Density % sol: 52 %
Description: PHASES WERE OBTAINED BY A SULFUR-SAD EXPERIMENT USING CU-K-ALPHA RADIATION FROM A RIGAKU FR-E SUPERBRIGHT X-RAY GENERATOR
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN AT 20 DEGRRES C USING THE VAPOR DIFFUSION METHOD IN HANGING DROP MODE BY MIXING 1 MICROLITER PROTEIN (20 MG/ML) IN 20 MM HEPES, PH 7.0, 0.1 M NACL, 2 MM BETA-OCTYL ...Details: CRYSTALS WERE GROWN AT 20 DEGRRES C USING THE VAPOR DIFFUSION METHOD IN HANGING DROP MODE BY MIXING 1 MICROLITER PROTEIN (20 MG/ML) IN 20 MM HEPES, PH 7.0, 0.1 M NACL, 2 MM BETA-OCTYL GLUCOSIDE WITH 1 MICROLITER RESERVOIR SOLUTION (10-12% (W/V) PEG 20K, 0.1 M MES, PH 6.5) AND EQUILIBRATING AGAINST 1 ML OF RESERVOIR SOLUTION. CRYSTALS APPEARED WITHIN SEVERAL HOURS AND GREW TO A FINAL SIZE OF 0.2 X 0.2 X 0.8 MM IN ABOUT 2 DAYS. THE CRYSTALS WERE CRYO-PROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.00869
DetectorType: CUSTOM / Detector: CCD / Date: Feb 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00869 Å / Relative weight: 1
ReflectionResolution: 1.78→31.04 Å / Num. obs: 39206 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.4
Reflection shellResolution: 1.78→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.78→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.687 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1893 5.1 %RANDOM
Rwork0.234 ---
obs0.236 35504 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 29 128 2732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9423759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75423.841138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49115437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1781513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21331
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21889
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.51692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07522664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65831231
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4154.51095
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 42
Rwork0.29 1065
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)
11.741-2.85271.62945.8312-3.35562.5227-0.367-0.2793-0.21790.07710.56330.2933-0.0498-0.3468-0.1964-0.1420.01680.0040.01480.0546-0.0766-3.253216.4998-9.1786
21.6035-1.92090.47724.0781-1.90531.4606-0.2004-0.1710.0209-0.0260.2788-0.0352-0.054-0.2935-0.0783-0.0998-0.0142-0.0809-0.01670.0149-0.1082-8.600730.4491-15.4555
31.055-2.1712-0.18188.478-0.6711.5465-0.0028-0.1538-0.0859-0.33010.047-0.24840.307-0.0194-0.0442-0.1728-0.0496-0.088-0.11950.0252-0.1268-3.140722.4842-16.0248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 132
2X-RAY DIFFRACTION2A133 - 261
3X-RAY DIFFRACTION3A262 - 325

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