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- PDB-6qvf: TT_C0855 competence pilin from Thermus thermophilus HB27 -

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Basic information

Entry
Database: PDB / ID: 6qvf
TitleTT_C0855 competence pilin from Thermus thermophilus HB27
ComponentsPrepilin-like protein
KeywordsDNA BINDING PROTEIN / Type IV pilin / natural competence
Function / homologyProkaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell outer membrane / periplasmic space / Prepilin-like protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.44 Å
AuthorsDerrick, J.P. / Salleh, M.Z. / Levy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093388/Z/10/Z United Kingdom
CitationJournal: Mbio / Year: 2019
Title: Structure and Properties of a Natural Competence-Associated Pilin Suggest a Unique Pilus Tip-Associated DNA Receptor.
Authors: Salleh, M.Z. / Karuppiah, V. / Snee, M. / Thistlethwaite, A. / Levy, C.W. / Knight, D. / Derrick, J.P.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Prepilin-like protein
B: Prepilin-like protein
C: Prepilin-like protein
D: Prepilin-like protein


Theoretical massNumber of molelcules
Total (without water)75,0324
Polymers75,0324
Non-polymers00
Water18,1231006
1
A: Prepilin-like protein
B: Prepilin-like protein


Theoretical massNumber of molelcules
Total (without water)37,5162
Polymers37,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Prepilin-like protein
D: Prepilin-like protein


Theoretical massNumber of molelcules
Total (without water)37,5162
Polymers37,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.588, 137.815, 59.739
Angle α, β, γ (deg.)90.000, 98.180, 90.000
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: 1 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA32 - 2013 - 172
21ARGARGBB32 - 2013 - 172
12ALAALAAA33 - 2014 - 172
22ALAALACC33 - 2014 - 172
13ARGARGAA32 - 2013 - 172
23ARGARGDD32 - 2013 - 172
14ALAALABB33 - 2014 - 172
24ALAALACC33 - 2014 - 172
15LEULEUBB31 - 2012 - 172
25LEULEUDD31 - 2012 - 172
16ALAALACC33 - 2014 - 172
26ALAALADD33 - 2014 - 172

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999997, -0.001931, -0.001437), (-0.002308, 0.938348, 0.345685), (0.000681, 0.345687, -0.93835)56.60302, -6.03092, 34.2253
3given(1), (1), (1)
4given(0.999985, 0.001065, 0.00534), (0.001039, -0.999987, 0.00498), (0.005345, -0.004975, -0.999973)-0.18892, 133.43457, 59.429852
5given(1), (1), (1)
6given(-0.999964, -0.001026, 0.008448), (-0.001944, -0.938914, -0.344145), (0.008285, -0.344149, 0.938878)56.255711, 139.70108, 24.53516
7given(1), (1), (1)
8given(-0.999986, 0.001042, -0.005157), (0.000775, -0.94034, -0.340235), (-0.005203, -0.340234, 0.940326)56.460651, 139.677155, 24.551109
9given(1), (1), (1)
10given(0.999976, 0.003315, -0.006066), (0.003329, -0.999992, 0.002173), (-0.006059, -0.002194, -0.999979)-0.04418, 133.37117, 59.47612
11given(1), (1), (1)
12given(-0.999913, -0.003639, 0.012674), (0.000873, 0.940782, 0.339011), (-0.013157, 0.338992, -0.940697)56.261372, -6.03466, 35.23877

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Components

#1: Protein
Prepilin-like protein


Mass: 18758.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: sequence GSGSWSHPQFEK corresponds to inserted linker and Strep tag
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: pilA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KPZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium nitrate, 0.1 M Bis-Tris propane pH 8.5, and 18% v/v PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.39→69 Å / Num. obs: 154421 / % possible obs: 86.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Net I/σ(I): 8.6
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 2.9 % / % possible all: 59.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.44→68.91 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.093 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.062
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 1703 1.3 %RANDOM
Rwork0.1513 ---
obs0.1518 128589 89.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.75 Å2 / Biso mean: 25.144 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0.4 Å2
2---1.17 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: final / Resolution: 1.44→68.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 0 1006 6180
Biso mean---36.95 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0145342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174627
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6727323
X-RAY DIFFRACTIONr_angle_other_deg1.0521.62510929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15719.851268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6691551
X-RAY DIFFRACTIONr_chiral_restr0.0790.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02954
X-RAY DIFFRACTIONr_rigid_bond_restr4.72339969
X-RAY DIFFRACTIONr_sphericity_free18.5645609
X-RAY DIFFRACTIONr_sphericity_bonded11.423510198
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A12774.06
2A12663.94
3A12775.2
4B12664.67
5B12854.25
6C12664.5
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 101 -
Rwork0.315 7410 -
all-7511 -
obs--69.95 %

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