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- PDB-7zcv: Rgg144 of Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 7zcv
TitleRgg144 of Streptococcus pneumoniae
ComponentsTranscriptional regulator
KeywordsDNA BINDING PROTEIN / quorum sensing protein / transcription regulator
Function / homology
Function and homology information


Transcription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWallis, R. / Girija, U.V. / Yesilkaya, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Mol.Microbiol. / Year: 2022
Title: Structure-function analysis for the development of peptide inhibitors for a Gram-positive quorum sensing system.
Authors: Abdullah, I.T. / Ulijasz, A.T. / Girija, U.V. / Tam, S. / Andrew, P. / Hiller, N.L. / Wallis, R. / Yesilkaya, H.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Transcriptional regulator
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)67,9722
Polymers67,9722
Non-polymers00
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-39 kcal/mol
Surface area26100 Å2
Unit cell
Length a, b, c (Å)75.479, 80.871, 106.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 5 through 287)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 287 / Label seq-ID: 5 - 287

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 5 through 287)BB

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Components

#1: Protein Transcriptional regulator


Mass: 33986.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: mutR, ERS021218_00146, ERS096071_01044, SAMEA3381574_00832, SAMEA3389353_01155
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E7KI02
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris propane pH 7.5, containing 200 mM potassium sodium tartrate tetrahydrate and PEG4K (18-26%)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→32.51 Å / Num. obs: 52047 / % possible obs: 99.91 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.031 / Mean I/σ(I) obs: 2 / Num. unique obs: 5148 / CC1/2: 0.526 / Rpim(I) all: 0.412

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.51 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 2565 4.93 %
Rwork0.1885 49481 -
obs0.1898 52046 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.5 Å2 / Biso mean: 44.2349 Å2 / Biso min: 19.45 Å2
Refinement stepCycle: final / Resolution: 1.9→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 0 410 5142
Biso mean---46.3 -
Num. residues----568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2747X-RAY DIFFRACTION7.911TORSIONAL
12B2747X-RAY DIFFRACTION7.911TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.940.34451370.303927322869
1.94-1.980.27811290.281227032832
1.98-2.020.30211410.256927162857
2.02-2.070.28951260.237127062832
2.07-2.120.25231580.227327102868
2.12-2.170.28151210.222627702891
2.17-2.240.24221450.206526832828
2.24-2.310.22651440.205927402884
2.31-2.390.22411480.196627012849
2.39-2.490.24341540.198927042858
2.49-2.60.22451260.200927912917
2.6-2.740.1991350.202127262861
2.74-2.910.23911400.202527572897
2.91-3.140.2381480.194427552903
3.14-3.450.23531790.186427312910
3.45-3.950.16661510.159427862937
3.95-4.970.18371530.150228072960
4.97-32.510.19121300.18229633093
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)
11.36670.0291-0.10986.4663-0.55381.3734-0.19580.0987-0.5337-0.14540.10220.01450.4038-0.12760.07360.3033-0.05550.10490.337-0.09290.422614.8775-8.51938.0115
24.29041.0105-1.15773.1308-1.85835.10530.06170.64710.4995-0.23760.27230.5238-0.4182-0.3995-0.28350.27050.0079-0.0120.27350.03640.29639.400621.680435.1266
33.35142.11550.58167.78842.68712.7925-0.09980.0184-0.06310.14550.1009-0.21240.0712-0.05620.01580.22870.010.00520.2038-0.00620.177419.497519.59247.1903
45.8397-5.6748-1.84216.89261.2034.84-0.6733-0.6024-0.24440.76680.73380.08780.7110.6554-0.09290.32780.0533-0.05960.3543-0.05030.230129.977620.229252.0346
53.7207-2.0235-0.76167.34983.79413.9866-0.17580.1340.2466-0.32480.2538-0.2692-0.30270.4542-0.08170.2586-0.0744-0.05520.21830.0390.165440.019827.983442.8623
66.2914-3.9871-3.58648.7658.76979.7606-0.0210.09420.3033-0.4787-0.14880.1356-0.3965-0.51250.13260.4375-0.0481-0.1420.37730.13060.336334.361932.248336.9465
75.40782.148-0.35516.01721.18053.459-0.32130.4644-0.3865-0.16360.21710.50750.2059-0.4610.06240.1928-0.080.05850.3121-0.05810.37320.5992-0.444941.8861
85.5879-2.53110.80031.83820.15541.0367-0.1819-0.8252-0.23870.74880.22920.07860.66530.4742-0.02360.62690.16490.00070.56840.02010.36628.6778-7.240752.0063
92.21140.6719-0.41632.90560.98682.0053-0.1514-0.2231-0.05930.08880.1517-0.03360.11370.35380.01450.24480.0781-0.03080.3321-0.05630.191642.0849-3.526835.5195
103.7467-5.0493-4.95948.77514.7149.0310.027-0.3334-0.63110.48790.0938-0.82280.41780.5737-0.13210.4141-0.0671-0.14360.6824-0.11280.588954.75272.674941.9167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 89 )A5 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 152 )A90 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 208 )A153 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 230 )A209 - 230
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 269 )A231 - 269
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 287 )A270 - 287
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 58 )B3 - 58
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 109 )B59 - 109
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 269 )B110 - 269
10X-RAY DIFFRACTION10chain 'B' and (resid 270 through 287 )B270 - 287

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