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- PDB-5g2f: Type IV-like competence pilin TTHA1222 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5g2f
TitleType IV-like competence pilin TTHA1222 from Thermus thermophilus
ComponentsTYPE-IV LIKE PILIN TTHA1222
KeywordsUNKNOWN FUNCTION / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE
Function / homology
Function and homology information


cell outer membrane / periplasmic space
Similarity search - Function
Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #70 / Pilin A4 / Pilin A4 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pilin, type IV, putative
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 7, 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 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: TYPE-IV LIKE PILIN TTHA1222
B: TYPE-IV LIKE PILIN TTHA1222
C: TYPE-IV LIKE PILIN TTHA1222
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6834
Polymers30,5873
Non-polymers961
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.380, 84.380, 97.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0801, 0.9963, 0.0321), (0.5013, 0.0681, -0.8626), (-0.8615, -0.053, -0.5049)
Vector: -39.1637, 38.0773, 47.7577)

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Components

#1: Protein TYPE-IV LIKE PILIN TTHA1222


Mass: 10195.503 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS / References: UniProt: Q5SIZ2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.83 Å3/Da / Density % sol: 56.57 % / Description: NONE
Crystal growDetails: 0.2M NA/K TARTRATE 0.1M SODIUM CITRATE PH 5.6 2.0 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9512
DetectorType: PILATUS / Detector: PIXEL / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9512 Å / Relative weight: 1
ReflectionResolution: 1.85→31.86 Å / Num. obs: 28582 / % possible obs: 99 % / Observed criterion σ(I): 3.1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.85→63.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.124 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20781 1965 7 %RANDOM
Rwork0.18248 ---
obs0.18421 26205 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 5 119 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021841
X-RAY DIFFRACTIONr_bond_other_d0.0050.021775
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9882513
X-RAY DIFFRACTIONr_angle_other_deg1.05334083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10924.37564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18815290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.661159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212067
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02376
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_it1.722.709980
X-RAY DIFFRACTIONr_mcbond_other1.7152.707979
X-RAY DIFFRACTIONr_mcangle_it2.5124.0431218
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4592.994861
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: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 132 -
Rwork0.257 1828 -
obs--92.54 %
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)
11.6169-0.28090.40221.83450.4112.51290.0567-0.0945-0.26610.3894-0.0006-0.2510.4268-0.0087-0.05610.1337-0.0024-0.0690.04980.01250.11378.469834.020714.6654
23.727-0.80340.52011.2196-0.05271.5184-0.00290.04570.2364-0.1006-0.00990.08490.0049-0.07950.01290.08060.009-0.06230.0071-0.00210.066722.686248.899421.7047
31.37120.28650.49161.07680.94153.8692-0.0460.6254-0.2275-0.48150.05420.15990.2408-0.1442-0.00810.3975-0.0547-0.10780.3333-0.12050.193632.407632.45868.5202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 123
2X-RAY DIFFRACTION2B38 - 123
3X-RAY DIFFRACTION3C41 - 120

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