[English] 日本語
Yorodumi
- PDB-4di4: Crystal structure of a 3:1 complex of Treponema pallidum TatP(T) ... -

+
Open data


ID or keywords:

Loading...

-
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / D-Maltodextrin-Binding Protein; domain 2 ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / D-Maltodextrin-Binding Protein; domain 2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more