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- PDB-5g25: Type IV-like pilin TTHA1218 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5g25
TitleType IV-like pilin TTHA1218 from Thermus thermophilus
ComponentsTYPE-IV LIKE COMPETENCE PILIN TTHA1218
KeywordsSTRUCTURAL PROTEIN / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE
Function / homology: / Type IV pilin Tt1218 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / cell outer membrane / Probable prepilin-like protein
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Jun 14, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE-IV LIKE COMPETENCE PILIN TTHA1218
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8022
Polymers10,7101
Non-polymers921
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.590, 156.590, 156.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein TYPE-IV LIKE COMPETENCE PILIN TTHA1218


Mass: 10710.224 Da / Num. of mol.: 1
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: Q5SIZ6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.73 Å3/Da / Density % sol: 67.06 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.0 1M SUCCINIC ACID 1% PEG 2000 MME

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I0210.9
SYNCHROTRONDiamond I0420.97
Detector
IDDate
1Oct 1, 2012
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.971
ReflectionResolution: 2.3→55.36 Å / Num. obs: 7765 / % possible obs: 99.9 % / Observed criterion σ(I): 3.6 / Redundancy: 11.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→90.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.483 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 356 4.6 %RANDOM
Rwork0.20828 ---
obs0.20962 7380 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.233 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→90.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 6 12 637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019633
X-RAY DIFFRACTIONr_bond_other_d0.0010.02625
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.993856
X-RAY DIFFRACTIONr_angle_other_deg0.65631432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.471581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55624.13829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96315108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.361157
X-RAY DIFFRACTIONr_chiral_restr0.0730.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
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_it4.4125.164327
X-RAY DIFFRACTIONr_mcbond_other4.4175.144326
X-RAY DIFFRACTIONr_mcangle_it5.9247.699407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0355.992306
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: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 23 -
Rwork0.225 528 -
obs--99.82 %

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