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- PDB-4di4: Crystal structure of a 3:1 complex of Treponema pallidum TatP(T) ... -

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Basic information

Entry
Database: PDB / ID: 4di4
TitleCrystal structure of a 3:1 complex of Treponema pallidum TatP(T) (Tp0957) bound to TatT (Tp0956)
Components
  • TatP(T) (Tp0957)
  • TatT (Tp0956)
KeywordsTRANSPORT PROTEIN / protein-protein complex / TRAP transporter / TPAT
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
TRAP transporter T-component / TRAP transporter T-component / TRAP transporter T-component superfamily / TRAP transporter T-component / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...TRAP transporter T-component / TRAP transporter T-component / TRAP transporter T-component superfamily / TRAP transporter T-component / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Uncharacterized protein TP_0956 / Tp33 protein
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum (syphilis treponeme)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.714 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural and Thermodynamic Characterization of the Interaction between Two Periplasmic Treponema pallidum Lipoproteins that are Components of a TPR-Protein-Associated TRAP Transporter (TPAT).
Authors: Brautigam, C.A. / Deka, R.K. / Schuck, P. / Tomchick, D.R. / Norgard, M.V.
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Structure summary / Category: entity / entity_name_com / software
Item: _entity.pdbx_description / _software.classification ..._entity.pdbx_description / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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: TatT (Tp0956)
B: TatP(T) (Tp0957)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3394
Polymers69,9952
Non-polymers3442
Water18010
1
A: TatT (Tp0956)
B: TatP(T) (Tp0957)
hetero molecules

A: TatT (Tp0956)
B: TatP(T) (Tp0957)
hetero molecules

A: TatT (Tp0956)
B: TatP(T) (Tp0957)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,01812
Polymers209,9856
Non-polymers1,0336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)172.879, 172.879, 150.718
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsThe biological unit is a heterohexamer generated from the heterodimer in the asymmetric unit using the operations: -y, x-y, z, and -x+y, -x, z

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Components

#1: Protein TatT (Tp0956)


Mass: 33716.078 Da / Num. of mol.: 1 / Fragment: soluble 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: TP_0956 / Plasmid: pE-SUMOpro3 / Production host: Escherichia coli (E. coli) / References: UniProt: O83922
#2: Protein TatP(T) (Tp0957) / TRAP-T family tripartite ATP-independent periplasmic transporter / binding protein


Mass: 36278.836 Da / Num. of mol.: 1 / Fragment: soluble fragment, UNP residues 21-342 / Mutation: A185V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme)
Strain: Nichols / Gene: TP_0957 / Plasmid: pGEM-T Easy / Production host: Escherichia coli (E. coli) / References: UniProt: O83923
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5
Details: 0.1 M CHES, 30% PEG400, pH 9.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: sagitally focused Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.714→50 Å / Num. all: 23479 / Num. obs: 23479 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Rmerge(I) obs: 0.083 / Χ2: 1.001 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.714-2.779.80.94811501.1651100
2.77-2.8211.60.91111581.0561100
2.82-2.8713.20.86811851.0341100
2.87-2.9314.40.71511421.0071100
2.93-2.9915.10.57811740.9891100
2.99-3.0615.40.4511531.0041100
3.06-3.1415.50.36411760.9761100
3.14-3.2215.40.30711631.0011100
3.22-3.3215.50.2211590.9981100
3.32-3.4315.40.17711691.0311100
3.43-3.5515.40.13711700.9841100
3.55-3.6915.40.10411701.0451100
3.69-3.8615.40.08311831.0431100
3.86-4.0615.30.07411570.9591100
4.06-4.3215.30.0611771.0311100
4.32-4.6515.30.05811760.9621100
4.65-5.1215.10.06211880.9741100
5.12-5.8615.10.07611831.0611100
5.86-7.3814.70.05912000.9761100
7.38-5014.20.03112460.807199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
SBC-CollectCOLLECTdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U64

3u64


Resolution: 2.714→43.436 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 1205 5.14 %RANDOM
Rwork0.1937 ---
obs0.1976 23458 99.72 %-
all-23458 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.504 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 173.72 Å2 / Biso mean: 81.3707 Å2 / Biso min: 25.81 Å2
Baniso -1Baniso -2Baniso -3
1-7.798 Å2-0 Å2-0 Å2
2--7.798 Å20 Å2
3----15.596 Å2
Refinement stepCycle: LAST / Resolution: 2.714→43.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 23 10 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084667
X-RAY DIFFRACTIONf_angle_d1.2066323
X-RAY DIFFRACTIONf_chiral_restr0.094702
X-RAY DIFFRACTIONf_plane_restr0.005804
X-RAY DIFFRACTIONf_dihedral_angle_d16.5091703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.714-2.82240.34431180.27122413253198
2.8224-2.95080.43951170.30824762593100
2.9508-3.10630.36561410.269324452586100
3.1063-3.30090.35451580.245924212579100
3.3009-3.55560.3061510.218224442595100
3.5556-3.91320.27021420.202824682610100
3.9132-4.4790.22761290.152424972626100
4.479-5.64110.23721210.162325072628100
5.6411-43.44130.23291280.176925822710100
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)
12.96120.09720.81754.1430.04241.03160.0417-0.31680.24590.2926-0.0080.1044-0.33230.054-0.00820.3711-0.00230.0140.3838-0.06130.4245-7.35065.171757.9865
23.67110.5471-0.96333.2402-0.29536.17590.17880.23030.05310.0598-0.2748-0.0222-0.30810.05120.04560.1761-0.04110.01160.3103-0.04160.463-15.25541.916950.1188
33.91840.764-0.43591.4442-0.72843.1807-0.03020.0848-0.1757-0.05450.0772-0.07730.5035-0.5665-0.0760.3144-0.02970.01320.3549-0.02670.3908-24.3407-5.309452.2382
45.13294.45221.64327.36553.70974.3725-0.0426-0.33930.65130.52770.03040.90280.0804-0.4978-0.06510.5004-0.02140.13690.74320.00090.5365-38.72140.621262.2225
51.93420.0586-0.36071.1111-0.11124.01110.00040.12240.3231-0.0348-0.0407-0.0109-0.0355-0.4030.0510.24650.02860.00630.41510.03770.4641-30.63564.82751.1522
63.6904-0.1779-2.09923.6977-0.23764.24520.08120.44650.5732-0.15450.21740.5428-0.3527-0.4568-0.28720.44210.07480.00030.48240.13830.5847-31.17415.892944.6145
74.3498-0.78030.86281.9817-0.05793.1736-0.31470.38370.6968-0.57750.3181-0.1596-0.52970.0726-0.11870.5787-0.1468-0.00610.35860.13860.5593-18.544419.06938.4582
82.1781.6926-1.80032.714-1.2311.935-0.4876-0.13350.0893-0.13930.4537-0.6244-0.09920.85140.05050.6635-0.15710.03270.9187-0.03830.3836-20.3793-0.683922.2603
91.98311.41330.03232.784-0.69481.5856-0.48830.929-0.0172-1.2880.30090.1288-0.32970.17520.07590.8955-0.2746-0.09010.95610.0770.2678-33.518-4.118215.1214
103.0963-1.7841-0.15751.49991.12092.2284-0.0430.55560.2289-0.8443-0.62220.4899-1.0341-0.87420.69040.8812-0.014-0.20890.9195-0.03530.6621-53.4896-9.18128.7836
113.50381.3353-0.64292.36680.08331.2632-0.07390.5385-0.2671-0.40240.21-0.1074-0.0425-0.072-0.12650.5386-0.1682-0.03940.87010.0170.4182-32.2671-9.957425.0524
123.47122.07630.27791.7440.73735.2193-0.41490.3117-0.3848-0.4029-0.1577-0.1669-0.0331-0.64150.41310.5267-0.10960.01970.7615-0.08430.6756-50.4081-20.674719.934
133.779-1.02730.45385.6879-1.36863.8778-0.31591.0659-0.2929-0.52410.21960.7675-0.78281.53030.03650.9318-0.3742-0.1221.47-0.06510.6174-43.0895-14.32925.9734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 29:62)A29 - 62
2X-RAY DIFFRACTION2chain 'A' and (resseq 63:96)A63 - 96
3X-RAY DIFFRACTION3chain 'A' and (resseq 97:137)A97 - 137
4X-RAY DIFFRACTION4chain 'A' and (resseq 138:152)A138 - 152
5X-RAY DIFFRACTION5chain 'A' and (resseq 153:211)A153 - 211
6X-RAY DIFFRACTION6chain 'A' and (resseq 212:249)A212 - 249
7X-RAY DIFFRACTION7chain 'A' and (resseq 250:301)A250 - 301
8X-RAY DIFFRACTION8chain 'B' and (resseq 9:39)B9 - 39
9X-RAY DIFFRACTION9chain 'B' and (resseq 40:143)B40 - 143
10X-RAY DIFFRACTION10chain 'B' and (resseq 144:193)B144 - 193
11X-RAY DIFFRACTION11chain 'B' and (resseq 194:276)B194 - 276
12X-RAY DIFFRACTION12chain 'B' and (resseq 277:306)B277 - 306
13X-RAY DIFFRACTION13chain 'B' and (resseq 307:323)B307 - 323

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