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- PDB-5u2p: The crystal structure of Tp0737 from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 5u2p
TitleThe crystal structure of Tp0737 from Treponema pallidum
ComponentsSugar ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / ligand-binding protein
Function / homologyBROMIDE ION / :
Function and homology information
Biological speciesTreponema pallidum subsp. pallidum (syphilis treponeme)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Norgard, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI056305 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Functional clues from the crystal structure of an orphan periplasmic ligand-binding protein from Treponema pallidum.
Authors: Brautigam, C.A. / Deka, R.K. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9315
Polymers47,7181
Non-polymers2134
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-14 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.925, 55.925, 237.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

#1: Protein Sugar ABC transporter substrate-binding protein


Mass: 47718.188 Da / Num. of mol.: 1 / Fragment: residues 28-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme)
Gene: A8P32_03680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3KAD9
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaBr 0.1 M Bis-Tris Propane 20% PEK 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→37.539 Å / Num. obs: 43052 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.6
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→37.539 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2171 5.04 %
Rwork0.1812 --
obs0.1832 43049 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→37.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 7 213 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083063
X-RAY DIFFRACTIONf_angle_d1.044177
X-RAY DIFFRACTIONf_dihedral_angle_d13.6941106
X-RAY DIFFRACTIONf_chiral_restr0.043489
X-RAY DIFFRACTIONf_plane_restr0.006537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7595-1.79780.28971340.24592425X-RAY DIFFRACTION94
1.7978-1.83960.28881470.21922466X-RAY DIFFRACTION99
1.8396-1.88560.24571330.21052571X-RAY DIFFRACTION99
1.8856-1.93660.24621380.20252565X-RAY DIFFRACTION99
1.9366-1.99360.21791450.19222534X-RAY DIFFRACTION99
1.9936-2.05790.23351330.1912545X-RAY DIFFRACTION99
2.0579-2.13140.19321380.18352529X-RAY DIFFRACTION98
2.1314-2.21680.22171410.17452546X-RAY DIFFRACTION98
2.2168-2.31760.22511340.17852588X-RAY DIFFRACTION99
2.3176-2.43980.22911250.17822565X-RAY DIFFRACTION99
2.4398-2.59260.25991090.182607X-RAY DIFFRACTION98
2.5926-2.79280.231490.18182579X-RAY DIFFRACTION98
2.7928-3.07370.20281300.18942551X-RAY DIFFRACTION98
3.0737-3.51820.23331530.18942577X-RAY DIFFRACTION97
3.5182-4.43140.19651320.16472591X-RAY DIFFRACTION96
4.4314-37.5470.21411300.17182639X-RAY DIFFRACTION92
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)
10.6690.16040.15190.3261-0.03860.17140.1403-0.0704-0.4590.1444-0.28730.51880.1219-0.1137-0.00060.29840.00030.0540.2884-0.01620.3987-17.612123.632460.2904
20.7238-0.40250.08571.0069-0.13380.24930.22540.11840.1233-0.2503-0.2175-0.2179-0.02960.055-0.01230.22560.06740.07550.1860.06120.196311.026917.640254.4153
30.3065-0.3554-0.01810.8119-0.17110.56750.06540.05560.0732-0.0789-0.1013-0.12860.07060.11580.00010.1840.03550.050.14810.02950.173610.492110.094762.646
40.5867-0.6078-0.08951.3267-0.46010.00940.1015-0.06670.0108-0.0716-0.1417-0.07510.1086-0.0266-0.06020.25970.10270.04210.11770.02580.15786.484718.015957.4276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 299 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 399 )

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