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- PDB-3u64: The Crystal Structure of Tat-T (Tp0956) -

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Basic information

Entry
Database: PDB / ID: 3u64
TitleThe Crystal Structure of Tat-T (Tp0956)
ComponentsProtein TP_0956
KeywordsTRANSPORT PROTEIN / Treponema pallidum / tetratrico peptide repeat / protein-protein interaction / syphilis / lipoprotein
Function / homologyTRAP transporter T-component / TRAP transporter T-component / TRAP transporter T-component superfamily / TRAP transporter T-component / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Uncharacterized protein TP_0956
Function and homology information
Biological speciesTreponema pallidum subsp. pallidum (syphilis treponeme)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter.
Authors: Deka, R.K. / Brautigam, C.A. / Goldberg, M. / Schuck, P. / Tomchick, D.R. / Norgard, M.V.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Protein TP_0956
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1005
Polymers33,7161
Non-polymers3844
Water1,06359
1
A: Protein TP_0956
hetero molecules

A: Protein TP_0956
hetero molecules

A: Protein TP_0956
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,30115
Polymers101,1483
Non-polymers1,15312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area5690 Å2
ΔGint-154 kcal/mol
Surface area38160 Å2
MethodPISA
2
A: Protein TP_0956
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)409,20460
Polymers404,59312
Non-polymers4,61148
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area32430 Å2
ΔGint-706 kcal/mol
Surface area142970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.078, 127.078, 127.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

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Components

#1: Protein Protein TP_0956


Mass: 33716.078 Da / Num. of mol.: 1 / Fragment: UNP residues 23-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme)
Strain: Nichols / Gene: tp0956, TP_0956 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83922
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 30% PEG-400, 0.1 M Bicine, 0.2 M MgCl2, pH 9.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97758 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97758 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15399 / % possible obs: 99.9 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.223 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3414.30.8997691.076199.7
2.34-2.3816.30.8017511.0551100
2.38-2.4317.40.7147761.051199.9
2.43-2.4818.40.5937531.044199.9
2.48-2.53190.5187491.07199.9
2.53-2.5919.50.427491.1451100
2.59-2.6619.80.3847661.129199.9
2.66-2.7319.70.3287791.3241100
2.73-2.8120.30.2467531.103199.9
2.81-2.920.20.1997891.2161100
2.9-320.30.1527541.2331100
3-3.1220.40.137621.281199.7
3.12-3.2620.30.1077801.2581100
3.26-3.44200.087591.281199.9
3.44-3.6519.90.0667711.4571100
3.65-3.9319.20.0567691.5481100
3.93-4.3319.80.0497871.327199.9
4.33-4.9519.50.0457721.23199.9
4.95-6.2418.90.0477841.272199.9
6.24-5019.90.0348271.23199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.953 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 0 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 758 4.97 %RANDOM
Rwork0.1967 ---
obs0.1989 15250 99.45 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.46 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 129.66 Å2 / Biso mean: 49.1898 Å2 / Biso min: 21.86 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 20 59 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082227
X-RAY DIFFRACTIONf_angle_d1.0063035
X-RAY DIFFRACTIONf_chiral_restr0.07329
X-RAY DIFFRACTIONf_plane_restr0.004391
X-RAY DIFFRACTIONf_dihedral_angle_d14.291788
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3003-2.47780.41081460.298628683014100
2.4778-2.7270.30351590.228728833042100
2.727-3.12120.31551380.22052881301999
3.1212-3.9310.23881570.19422886304399
3.931-29.95510.18691580.16872974313299
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)
11.791-0.52180.44813.11951.33881.95620.34470.11770.04630.1577-0.2681-0.5129-0.0740.3077-0.10010.3790.00450.05760.30460.00470.301927.4098-15.11179.9572
20.41320.29180.23310.30520.14560.5203-0.04560.01340.02010.07770.05250.0599-0.0674-0.0482-0.01130.3041-0.00650.00960.3136-0.01390.310217.2526-24.63865.4653
34.0502-1.0231.8711.7632-0.99846.4303-0.1672-0.4481-0.0662-0.13030.00580.30191.28960.19050.09050.44290.16560.08850.35360.06360.302828.6421-38.755717.296
41.3718-0.30350.34310.80710.88151.35580.03240.1303-0.11940.0987-0.03820.11790.1831-0.13240.06590.2585-0.005-0.01560.3297-0.05020.294816.6071-35.3241-8.0257
53.4905-0.3841.15210.62420.26484.98730.10430.2949-0.7162-0.232-0.0960.07520.97270.0093-0.04150.35470.0088-0.01990.1899-0.02240.344123.9059-41.272-5.873
63.27240.22151.70033.05360.26890.86470.0140.7217-0.18480.13750.1870.09710.04210.4028-0.19080.2460.04270.0140.4188-0.07990.253834.9577-35.409-8.7521
70.53310.46120.60712.2170.74751.2207-0.21170.30080.0809-0.21920.4198-0.1295-0.21630.4775-0.16360.31240.0776-0.0430.46860.00640.375745.2862-29.75031.3806
80.66140.2469-0.12770.9429-0.43490.3086-0.0153-0.0526-0.0477-0.07860.1054-0.01910.00280.0009-0.04620.36860.0131-0.07240.38270.01560.294641.1551-28.78318.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 30:46)A30 - 46
2X-RAY DIFFRACTION2(chain A and resid 47:88)A47 - 88
3X-RAY DIFFRACTION3(chain A and resid 89:108)A89 - 108
4X-RAY DIFFRACTION4(chain A and resid 109:166)A109 - 166
5X-RAY DIFFRACTION5(chain A and resid 167:192)A167 - 192
6X-RAY DIFFRACTION6(chain A and resid 193:234)A193 - 234
7X-RAY DIFFRACTION7(chain A and resid 235:273)A235 - 273
8X-RAY DIFFRACTION8(chain A and resid 274:300)A274 - 300

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