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- PDB-6qvi: Crystal structure of competence-associated pilin ComZ from Thermu... -

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Basic information

Entry
Database: PDB / ID: 6qvi
TitleCrystal structure of competence-associated pilin ComZ from Thermus thermophilus
ComponentsComZ
KeywordsDNA BINDING PROTEIN / competence pilin / DNA receptor / beta-solenoid domain / pseudopilin-like domain
Function / homologymembrane / ComZ
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsKaruppiah, V. / Derrick, J.P.
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
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ComZ
B: ComZ
C: ComZ


Theoretical massNumber of molelcules
Total (without water)172,4553
Polymers172,4553
Non-polymers00
Water27015
1
A: ComZ


Theoretical massNumber of molelcules
Total (without water)57,4851
Polymers57,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ComZ


Theoretical massNumber of molelcules
Total (without water)57,4851
Polymers57,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ComZ


Theoretical massNumber of molelcules
Total (without water)57,4851
Polymers57,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.860, 121.860, 212.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ComZ


Mass: 57485.031 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: comZ, TT_C0857 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72JC1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→58.79 Å / Num. obs: 49699 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 73.87 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 2.72→2.79 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.72→58.79 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30
RfactorNum. reflection% reflection
Rfree0.267 2514 5.07 %
Rwork0.206 --
obs0.209 49626 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.72→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11505 0 0 15 11520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211845
X-RAY DIFFRACTIONf_angle_d1.55116081
X-RAY DIFFRACTIONf_dihedral_angle_d8.4087012
X-RAY DIFFRACTIONf_chiral_restr0.0831794
X-RAY DIFFRACTIONf_plane_restr0.0092136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7201-2.77240.43571340.36152586X-RAY DIFFRACTION100
2.7724-2.8290.38161370.33592584X-RAY DIFFRACTION100
2.829-2.89050.37231430.30122561X-RAY DIFFRACTION100
2.8905-2.95770.34111320.28482583X-RAY DIFFRACTION100
2.9577-3.03170.3431300.26432603X-RAY DIFFRACTION100
3.0317-3.11360.33221550.25942578X-RAY DIFFRACTION100
3.1136-3.20530.32351460.24242582X-RAY DIFFRACTION100
3.2053-3.30870.3161430.23612583X-RAY DIFFRACTION100
3.3087-3.4270.29531080.22842616X-RAY DIFFRACTION100
3.427-3.56410.26751470.21832600X-RAY DIFFRACTION100
3.5641-3.72630.29011110.20822625X-RAY DIFFRACTION100
3.7263-3.92280.26541470.20812618X-RAY DIFFRACTION100
3.9228-4.16850.26671530.18562598X-RAY DIFFRACTION100
4.1685-4.49020.26431530.17652633X-RAY DIFFRACTION100
4.4902-4.94190.22071550.14682613X-RAY DIFFRACTION100
4.9419-5.65650.22421540.17522648X-RAY DIFFRACTION100
5.6565-7.12460.26941510.21632661X-RAY DIFFRACTION100
7.1246-58.79890.23521150.20112840X-RAY DIFFRACTION99
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)
15.63011.11012.35392.19060.70963.18020.03820.4189-0.0440.24050.0030.08741.01040.2966-0.00410.85270.11690.07210.2628-0.01120.416939.594831.4745120.3695
26.38410.3175-2.21672.08270.95412.4168-0.42950.5978-0.82060.2978-0.04880.07190.4448-0.30450.39280.4392-0.10060.1190.7489-0.05760.47243.100530.555677.5772
30.4030.52140.94861.40252.31683.1604-0.34360.265-0.00490.0297-0.28030.17030.4542-0.32590.73150.44640.00320.02050.60810.07940.477342.715133.7461101.9074
42.30170.8787-0.36872.6773-0.66855.71460.1974-0.1373-0.210.1633-0.21260.67710.0254-0.6289-0.06180.4125-0.1802-0.0480.5451-0.03340.702348.936114.113-6.8009
52.2920.90210.60323.90641.00661.9602-0.1939-0.03-0.4618-0.01960.11150.18980.643-0.71090.10930.895-0.4720.19571.2183-0.07650.644252.643716.904734.5779
60.70170.0094-1.79870.4014-1.09435.4373-0.1352-0.258-0.44230.4105-0.30590.17980.7079-0.42370.33010.8596-0.42830.12260.8660.06630.848853.243913.238920.1975
71.4747-0.6571-0.37380.3173-0.4232.38780.4432-0.1423-0.0870.2539-0.00450.3841-0.47880.0182-0.29621.3181-0.30550.20410.5179-0.05630.7311-3.021322.131798.0803
82.23230.6619-0.15957.2017-0.01013.92380.007-0.18030.434-0.4435-0.29650.65650.23510.41250.3320.64160.3194-0.2360.7601-0.27650.7952-3.059920.006156.5566
91.25490.24092.45310.4837-1.13435.75430.1856-0.1890.20970.5415-0.73050.2277-0.1061-0.23860.45681.1693-0.09770.0990.7679-0.27390.648-0.499719.103181.1191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 128 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 129 THROUGH 488 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 489 THROUGH 528 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 139 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 140 THROUGH 476 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 477 THROUGH 526 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 1 THROUGH 139 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 140 THROUGH 489 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 490 THROUGH 527 )

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