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- PDB-5g24: Type IV-like pilin TTHA1219 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5g24
TitleType IV-like pilin TTHA1219 from Thermus thermophilus
ComponentsTYPE-IV LIKE PILIN TTHA1219
KeywordsSTRUCTURAL PROTEIN / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE
Function / homology: / Type IV pilin Tt1219 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / cell outer membrane / Probable general secretion pathway protein J
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKaruppiah, V. / Derrick, J.P.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structures of Type Iv Pilins from Thermus Thermophilus Demonstrate Similarities with Type II Secretion System Pseudopilins
Authors: Karuppiah, V. / Thistlethwaite, A. / Derrick, J.P.
History
DepositionApr 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE-IV LIKE PILIN TTHA1219
B: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)50,2532
Polymers50,2532
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-4.9 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.830, 32.170, 108.120
Angle α, β, γ (deg.)90.00, 115.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4715, 0.1321, 0.8719), (0.0403, -0.9845, 0.1709), (0.881, 0.1157, 0.4588)
Vector: -73.5961, -26.5404, 46.7514)

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Components

#1: Protein TYPE-IV LIKE PILIN TTHA1219


Mass: 25126.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS / References: UniProt: Q5SIZ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growDetails: 0.01M ZINC CHLORIDE, 0.1M SODIUM ACETATE PH 5 AND 20% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→57.77 Å / Num. obs: 16586 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G23

5g23


Resolution: 2.3→97.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.194 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24034 838 5.1 %RANDOM
Rwork0.1901 ---
obs0.19266 15747 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.06 Å2
2---0.42 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→97.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 0 79 3016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192999
X-RAY DIFFRACTIONr_bond_other_d0.010.022878
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9864080
X-RAY DIFFRACTIONr_angle_other_deg1.56236605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81923.008123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96215463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0271530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213442
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02664
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.872.0881572
X-RAY DIFFRACTIONr_mcbond_other1.8672.0851571
X-RAY DIFFRACTIONr_mcangle_it3.0063.1171958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3552.4011427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 50 -
Rwork0.273 1126 -
obs--99.07 %
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)
12.49360.6776-0.21641.4296-0.12552.32590.1062-0.4644-0.25260.1852-0.1443-0.12170.07170.11110.03810.167-0.02250.04480.17110.03260.0577-26.871-11.38116.691
21.67190.0942-0.51991.547-0.43466.3916-0.0306-0.13230.10110.010.068-0.0986-0.0641-0.3679-0.03750.11390.01480.05870.27190.00450.047-47.673-11.73130.482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 236
2X-RAY DIFFRACTION2B39 - 236

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