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- PDB-5ukh: Structure of TelC from Streptococcus intermedius B196 -

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Basic information

Entry
Database: PDB / ID: 5ukh
TitleStructure of TelC from Streptococcus intermedius B196
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Antibacterial effector protein / Lipid II phosphatase / Type VII secretion / Esx secretion
Function / homologyLXG domain / LXG domain of WXG superfamily / LXG domain profile. / metal ion binding / LXG domain-containing protein
Function and homology information
Biological speciesStreptococcus intermedius B196 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsWhitney, J.C. / Ching, M.Q. / Bryant, D. / Mougous, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI080609 United States
CitationJournal: Elife / Year: 2017
Title: A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria.
Authors: Whitney, J.C. / Peterson, S.B. / Kim, J. / Pazos, M. / Verster, A.J. / Radey, M.C. / Kulasekara, H.D. / Ching, M.Q. / Bullen, N.P. / Bryant, D. / Goo, Y.A. / Surette, M.G. / Borenstein, E. / ...Authors: Whitney, J.C. / Peterson, S.B. / Kim, J. / Pazos, M. / Verster, A.J. / Radey, M.C. / Kulasekara, H.D. / Ching, M.Q. / Bullen, N.P. / Bryant, D. / Goo, Y.A. / Surette, M.G. / Borenstein, E. / Vollmer, W. / Mougous, J.D.
History
DepositionJan 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0564
Polymers41,9361
Non-polymers1203
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-21 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.383, 132.689, 58.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-602-

CA

21A-603-

CA

31A-714-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 41935.555 Da / Num. of mol.: 1 / Fragment: UNP residues 201-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius B196 (bacteria)
Gene: SIR_1489 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZG69
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Acetate pH 4.6, 0.1 M CaCl2, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→49.2 Å / Num. obs: 34824 / % possible obs: 100 % / Redundancy: 25.6 % / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→49.2 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.28
RfactorNum. reflection% reflection
Rfree0.2451 1740 5.69 %
Rwork0.2215 --
obs0.2228 30558 87.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 3 154 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082586
X-RAY DIFFRACTIONf_angle_d0.8843492
X-RAY DIFFRACTIONf_dihedral_angle_d12.8791540
X-RAY DIFFRACTIONf_chiral_restr0.044375
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.03830.45871170.45451926X-RAY DIFFRACTION72
2.0383-2.10410.44421200.41472043X-RAY DIFFRACTION75
2.1041-2.17930.33661450.35322176X-RAY DIFFRACTION81
2.1793-2.26650.37511360.3132223X-RAY DIFFRACTION82
2.2665-2.36970.32461380.27942276X-RAY DIFFRACTION84
2.3697-2.49460.26171360.25062333X-RAY DIFFRACTION86
2.4946-2.65090.25881460.23032452X-RAY DIFFRACTION90
2.6509-2.85560.2591510.22282499X-RAY DIFFRACTION92
2.8556-3.14290.28141540.22732558X-RAY DIFFRACTION94
3.1429-3.59760.24941550.19992697X-RAY DIFFRACTION98
3.5976-4.5320.19491700.17172748X-RAY DIFFRACTION99
4.532-49.21820.18551720.18762887X-RAY DIFFRACTION100
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)
16.05830.8736-1.00853.4174-0.79112.74030.3985-0.6489-0.75340.6187-0.1183-0.97150.87381.1817-0.18810.84480.1738-0.12910.6499-0.03070.451543.305141.90750.9509
22.34-0.0637-1.62882.3883-0.76675.28240.16830.36850.3518-0.3242-0.0052-0.3228-0.32480.3074-0.14420.56170.0255-0.00690.30250.03580.359839.999955.053531.5621
32.417-1.0584-2.44933.0781.14674.1331-0.29540.3201-0.24230.0401-0.0650.30830.5841-0.50410.34390.72870.0192-0.00970.3566-0.02370.286928.507231.846736.5763
44.26422.6918-2.50957.0809-1.48986.2380.2063-0.03560.18380.9008-0.1968-0.1719-0.76190.1575-0.070.57040.1043-0.01270.307-0.01550.27227.26848.914945.128
54.25420.3732-1.61084.31410.7782.1922-0.07620.23040.29210.0020.11560.0843-0.2889-0.1506-0.00630.74830.0683-0.05340.2682-0.00150.281726.607854.399649.1396
67.72310.8644.22451.41660.20292.2899-0.2014-0.56410.48660.3761-0.04220.3248-0.0682-0.58070.23070.70760.04420.04010.5388-0.12770.41310.766756.013954.4811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 212 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 328 )
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 413 )
5X-RAY DIFFRACTION5chain 'A' and (resid 414 through 488 )
6X-RAY DIFFRACTION6chain 'A' and (resid 489 through 550 )

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