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- PDB-6det: The crystal structure of Tv2483 bound to L-arginine -

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Basic information

Entry
Database: PDB / ID: 6det
TitleThe crystal structure of Tv2483 bound to L-arginine
ComponentsTv2483
KeywordsTRANSPORT PROTEIN / ABC transporter / amino-acid-binding protein / ligand-binding protein
Function / homologyBacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Prokaryotic membrane lipoprotein lipid attachment site profile. / ARGININE / Solute-binding protein family 3/N-terminal domain-containing protein
Function and homology information
Biological speciesTreponema vincentii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsBrautigam, C.A. / 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: 2018
Title: Biophysical insights into a highly selective l-arginine-binding lipoprotein of a pathogenic treponeme.
Authors: Deka, R.K. / Liu, W.Z. / Tso, S.C. / Norgard, M.V. / Brautigam, C.A.
History
DepositionMay 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Tv2483
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3722
Polymers30,1971
Non-polymers1751
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, assembly determined using analytical ultracentrifugation in sedimentation velocity mode.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.586, 130.436, 48.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21A-640-

HOH

31A-674-

HOH

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Components

#1: Protein Tv2483


Mass: 30197.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema vincentii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: S3MDF0
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% (v/v) isopropanol, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97953 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.75→81.6 Å / Num. obs: 33458 / % possible obs: 97.8 % / Redundancy: 4.4 % / Net I/σ(I): 22.4
Reflection shellResolution: 1.75→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.75→42.002 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.95
RfactorNum. reflection% reflection
Rfree0.1989 1667 5.06 %
Rwork0.1767 --
obs0.1779 32941 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→42.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 12 100 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011979
X-RAY DIFFRACTIONf_angle_d0.9762690
X-RAY DIFFRACTIONf_dihedral_angle_d12.8681194
X-RAY DIFFRACTIONf_chiral_restr0.059314
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7504-1.80190.27561100.24262306X-RAY DIFFRACTION87
1.8019-1.86010.27111430.22882476X-RAY DIFFRACTION93
1.8601-1.92660.27971240.22222549X-RAY DIFFRACTION96
1.9266-2.00370.22711350.2042640X-RAY DIFFRACTION98
2.0037-2.09490.22011570.19432602X-RAY DIFFRACTION98
2.0949-2.20540.241310.18752549X-RAY DIFFRACTION94
2.2054-2.34350.20931590.18082649X-RAY DIFFRACTION99
2.3435-2.52440.19571400.18232676X-RAY DIFFRACTION99
2.5244-2.77840.20741510.18872676X-RAY DIFFRACTION99
2.7784-3.18040.22721240.19312594X-RAY DIFFRACTION95
3.1804-4.00640.19791430.17382761X-RAY DIFFRACTION100
4.0064-42.01390.15841500.14852796X-RAY DIFFRACTION97
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)
16.80.0915-0.75871.55940.01751.141-0.4020.2161-0.3354-0.21080.0813-0.23510.25650.02820.31510.3734-0.0250.16150.2789-0.07250.471836.615911.24241.0306
25.3411.4187-2.24845.6236-1.94381.4623-0.17570.6122-0.4281-0.63770.15540.09230.10460.011-0.00880.3822-0.05080.08060.3359-0.12030.294928.665612.9366-6.8868
33.01810.2383-0.86862.7761-0.12992.2832-0.3018-0.0872-0.5227-0.00950.0181-0.26540.23920.09650.29390.2697-0.00530.10870.2333-0.01480.332733.435312.14988.7379
44.15730.5707-1.44893.3485-1.4783.8851-0.2233-0.421-0.17850.30120.30170.319-0.0721-0.4888-0.02480.29060.04020.12450.3975-0.00650.355210.532515.501317.3711
59.1598-0.413-6.49522.8202-2.35649.35660.0101-1.43420.02590.91470.16350.6332-0.07250.75530.0220.3417-0.01430.16360.5582-0.00840.504413.153312.401223.7443
65.56360.8286-1.19431.83030.05641.9832-0.01050.2594-0.45960.0626-0.11560.34730.1023-0.49980.1060.2862-0.01860.08040.335-0.07320.337715.087614.64649.3509
72.28920.04150.39841.5621-0.12871.7217-0.02580.368-0.1785-0.33160.0364-0.1092-0.01530.10680.03470.3712-0.06330.06530.3169-0.0660.297832.038523.852-3.8431
85.63840.11193.48519.1581.89369.0946-0.3613-0.102-0.0540.31760.2225-0.4617-0.22-0.13290.02340.2925-0.01680.00150.2361-0.01650.230127.379629.78172.5982
93.89472.5707-1.62324.69290.13993.6775-0.6918-0.0063-0.9086-0.15880.0570.04690.57610.43240.64370.3766-0.07580.12260.355-0.04080.329523.115712.34219.8254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 207 )
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 235 )
8X-RAY DIFFRACTION8chain 'A' and (resid 236 through 246 )
9X-RAY DIFFRACTION9chain 'A' and (resid 500 through 500 )

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