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- PDB-5g23: Type IV-like pilin TTHA1219 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5g23
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 / SIRAS / 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 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 TTHA1219
B: TYPE-IV LIKE PILIN TTHA1219
C: TYPE-IV LIKE PILIN TTHA1219
D: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)100,5074
Polymers100,5074
Non-polymers00
Water10,016556
1
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5.8 kcal/mol
Surface area16260 Å2
MethodPISA
2
C: TYPE-IV LIKE PILIN TTHA1219
D: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)50,2532
Polymers50,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-6.3 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 66.950, 97.470
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA43 - 23543 - 235
21GLYGLYALAALABB43 - 23543 - 235
12GLYGLYARGARGAA43 - 23643 - 236
22GLYGLYARGARGCC43 - 23643 - 236
13GLYGLYARGARGAA43 - 23643 - 236
23GLYGLYARGARGDD43 - 23643 - 236
14ARGARGALAALABB42 - 23542 - 235
24ARGARGALAALACC42 - 23542 - 235
15ARGARGALAALABB42 - 23542 - 235
25ARGARGALAALADD42 - 23542 - 235
16ARGARGARGARGCC42 - 23642 - 236
26ARGARGARGARGDD42 - 23642 - 236

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.4911, -0.2417, -0.8369), (-0.3263, -0.9418, 0.0805), (-0.8077, 0.2335, -0.5414)32.815, 26.4601, 49.7223
2given(0.5817, -0.0364, -0.8126), (-0.0837, -0.9964, -0.0153), (-0.8091, 0.0769, -0.5826)28.2388, 57.198, 44.1757
3given(0.9873, 0.1274, 0.0952), (-0.1402, 0.9796, 0.1436), (-0.0749, -0.1551, 0.985)-2.9444, -32.8189, 12.3465

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Components

#1: Protein
TYPE-IV LIKE PILIN TTHA1219


Mass: 25126.736 Da / Num. of mol.: 4
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.: 556 / 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: 2.45 Å3/Da / Density % sol: 49.7 % / 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: I24 / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→35.94 Å / Num. obs: 70620 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
autoSHARPmodel building
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
autoSHARPphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.85→96.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.489 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20878 3564 5 %RANDOM
Rwork0.18025 ---
obs0.18173 67037 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-1.09 Å2
2--0.33 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 0 556 6264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195832
X-RAY DIFFRACTIONr_bond_other_d0.0110.025581
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9867939
X-RAY DIFFRACTIONr_angle_other_deg1.665312823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90523.362232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0211551
X-RAY DIFFRACTIONr_chiral_restr0.1010.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216699
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021276
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_it1.6131.9063073
X-RAY DIFFRACTIONr_mcbond_other1.6121.9043072
X-RAY DIFFRACTIONr_mcangle_it2.6582.8423829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0562.1492759
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207320.13
12B207320.13
21A211000.11
22C211000.11
31A204800.14
32D204800.14
41B206400.13
42C206400.13
51B206100.13
52D206100.13
61C201880.15
62D201880.15
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 266 -
Rwork0.266 4955 -
obs--99.81 %
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)
11.18320.026-0.32561.10160.21661.7881-0.0690.0161-0.04590.08560.01990.01910.0658-0.07760.04910.04180.0005-0.01450.0043-0.00250.015122.357415.483636.2148
21.3329-0.25370.09621.20940.16460.7855-0.0165-0.02430.07830.0602-0.00120.073-0.0363-0.01350.01770.0171-0.0058-0.00370.00420.00220.01579.59029.904715.324
31.5408-0.0135-0.17991.0119-0.05190.91360.0042-0.05080.07580.05920.02030.0506-0.0328-0.0212-0.02440.0236-0.0028-0.00660.0040.00140.0126.710141.0110.0437
41.03260.09290.18591.23260.22541.3733-0.0141-0.0722-0.04670.0577-0.03680.0509-0.0381-0.07460.05090.06290.0007-0.03250.01320.00040.026516.47846.838332.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 236
2X-RAY DIFFRACTION2B42 - 235
3X-RAY DIFFRACTION3C42 - 236
4X-RAY DIFFRACTION4D40 - 236

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