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- PDB-5vfa: RitR Mutant - C128D -

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Basic information

Entry
Database: PDB / ID: 5vfa
TitleRitR Mutant - C128D
ComponentsResponse regulator
KeywordsTRANSCRIPTION / Repressor of iron transporter / Aspartate-less receiver domain protein / Transcription regulator / monomer
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 Å
AuthorsHan, L. / Silvaggi, N.R.
CitationJournal: PLoS Pathog. / Year: 2018
Title: RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization.
Authors: Glanville, D.G. / Han, L. / Maule, A.F. / Woodacre, A. / Thanki, D. / Abdullah, I.T. / Morrissey, J.A. / Clarke, T.B. / Yesilkaya, H. / Silvaggi, N.R. / Ulijasz, A.T.
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator
B: Response regulator


Theoretical massNumber of molelcules
Total (without water)53,9742
Polymers53,9742
Non-polymers00
Water10,106561
1
A: Response regulator


Theoretical massNumber of molelcules
Total (without water)26,9871
Polymers26,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator


Theoretical massNumber of molelcules
Total (without water)26,9871
Polymers26,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.836, 59.708, 52.509
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21B-470-

HOH

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Components

#1: Protein Response regulator /


Mass: 26987.211 Da / Num. of mol.: 2 / Mutation: C128D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: csrR, spr0336 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DR53
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.5, 22.5% Jeffamine ED-2001 pH 7.0 / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 76689 / % possible obs: 99 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.6
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3384 / CC1/2: 0.787 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2450: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u8k
Resolution: 1.452→27.519 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 2000 2.61 %Random selection
Rwork0.1635 ---
obs0.164 76664 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.452→27.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 0 561 4208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083718
X-RAY DIFFRACTIONf_angle_d0.9545004
X-RAY DIFFRACTIONf_dihedral_angle_d20.1191435
X-RAY DIFFRACTIONf_chiral_restr0.073571
X-RAY DIFFRACTIONf_plane_restr0.006630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4516-1.48790.27571260.24884722X-RAY DIFFRACTION88
1.4879-1.52810.27371410.23215246X-RAY DIFFRACTION97
1.5281-1.57310.21251430.21265322X-RAY DIFFRACTION100
1.5731-1.62380.24521430.20055349X-RAY DIFFRACTION100
1.6238-1.68180.23451450.19345408X-RAY DIFFRACTION100
1.6818-1.74920.21081430.18335369X-RAY DIFFRACTION100
1.7492-1.82880.23411450.18615366X-RAY DIFFRACTION100
1.8288-1.92520.17371440.16945390X-RAY DIFFRACTION100
1.9252-2.04570.19091440.16645398X-RAY DIFFRACTION100
2.0457-2.20360.18181440.15725392X-RAY DIFFRACTION100
2.2036-2.42530.18761450.15375388X-RAY DIFFRACTION100
2.4253-2.77590.16321450.15675418X-RAY DIFFRACTION100
2.7759-3.49630.18171460.15295448X-RAY DIFFRACTION100
3.4963-27.52430.15721460.14975448X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.53730.74830.23712.021-0.50563.06370.05180.07150.27210.03590.0091-0.1662-0.0290.0163-0.07160.14350.0370.0210.2014-0.02150.2239174.538776.906-7.6085
23.08551.347-0.2215.5376-0.71272.2501-0.0057-0.0898-0.5018-0.14290.0003-0.42590.22780.2039-0.00290.19140.0551-0.02350.2113-0.03030.268173.640966.9739-2.8883
32.324-0.13620.20891.40870.04171.12850.0267-0.10620.10460.09840.0216-0.00220.0641-0.0244-0.03940.1650.0120.0120.1445-0.01070.1568161.845574.1372-2.5843
45.47370.056-2.48780.2019-0.01861.1274-0.3148-0.3923-0.04210.27950.1743-0.2185-0.15650.21680.11420.32390.0108-0.07570.33-0.02160.186156.601967.63520.4617
51.681-0.8324-0.66852.62970.1130.88630.0699-0.31230.18580.13360.0356-0.16040.01920.0758-0.09160.1652-0.0236-0.04120.2373-0.06040.1538152.987574.746814.4959
64.19590.6018-0.66592.41830.3171.8640.09460.09820.3955-0.07480.0807-0.121-0.1242-0.002-0.16570.140.0068-0.00510.1495-0.01980.1296150.698779.55486.5017
70.88731.4820.34997.5665-0.51370.37970.0289-0.17150.02310.2670.02940.25580.11590.04760.0310.1786-0.0130.02050.1828-0.00070.129140.029670.179915.4776
82.91470.4911-0.51041.9740.73360.4541-0.0135-0.31920.16610.2687-0.0050.1405-0.0141-0.01610.04190.1983-0.01660.00580.2223-0.04450.1609141.085678.915317.9573
92.11790.82880.32651.8691-0.06452.6709-0.01580.04460.1406-0.04010.0522-0.0644-0.03360.1049-0.02570.1486-0.02210.0350.2073-0.04840.2258171.9959106.581718.8233
103.04450.5411-0.37944.8039-0.5263.4471-0.0887-0.1455-0.5032-0.28080.0847-0.38370.23970.40890.00040.16930.02560.02550.2075-0.03050.2592172.103697.227924.8052
112.67280.65980.14661.6166-0.27391.78130.0410.0114-0.22670.08180.0883-0.0440.16820.2032-0.09220.1824-0.00040.00930.1669-0.03710.2041164.472397.568622.9207
122.34990.5897-0.34742.3998-1.11762.7831-0.05020.08370.0031-0.040.15640.28650.0573-0.2346-0.13280.1403-0.01580.01950.1276-0.00920.2035156.4093100.649921.8735
131.38930.292-1.53230.7736-0.67494.12110.0783-0.03890.16840.09410.049-0.0384-0.0813-0.0419-0.16390.1736-0.02260.04120.1839-0.07150.3012162.9211113.562229.2367
143.9152-0.1024-1.5460.4415-0.37142.1389-0.0662-0.31580.32980.57830.2351-0.2415-0.15560.2109-0.05490.34120.0466-0.0390.2136-0.04160.2978156.289101.288447.2567
151.1773-0.5862-0.01852.0826-0.05250.8398-0.1143-0.1232-0.09730.08510.0951-0.04150.05580.0577-0.0010.16120.00970.0270.1617-0.00460.1442150.4714105.140540.8502
162.7306-0.6012-0.44412.47930.64721.4639-0.05670.1874-0.34390.00710.05320.36480.0081-0.1266-0.02210.15820.0105-0.00720.1528-0.02130.1992144.4951105.184335.1571
172.6339-0.04670.01022.01140.12781.2059-0.1821-0.2112-0.03410.3104-0.0280.38580.0781-0.06040.15030.21890.02210.05910.176-0.00620.2232138.4959108.380744.5702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 220 )
8X-RAY DIFFRACTION8chain 'A' and (resid 221 through 230 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 25 )
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 44 )
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 60 )
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 124 )
14X-RAY DIFFRACTION14chain 'B' and (resid 125 through 147 )
15X-RAY DIFFRACTION15chain 'B' and (resid 148 through 185 )
16X-RAY DIFFRACTION16chain 'B' and (resid 186 through 220 )
17X-RAY DIFFRACTION17chain 'B' and (resid 221 through 230 )

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