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- PDB-7rgs: The crystal structure of RocC, containing FinO domain, 24-126 -

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Basic information

Entry
Database: PDB / ID: 7rgs
TitleThe crystal structure of RocC, containing FinO domain, 24-126
ComponentsRepressor of competence, RNA Chaperone
KeywordsRNA BINDING PROTEIN / RNA chaperone / FinO / ProQ
Function / homologyRNA chaperone ProQ / RNA strand-exchange activity / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / RNA strand annealing activity / post-transcriptional regulation of gene expression / ProP effector
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKim, H.J. / Edwards, R.A. / Glover, J.N.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.
Authors: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / ...Authors: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / Tollinger, M. / Charpentier, X. / Attaiech, L. / Glover, J.N.M.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repressor of competence, RNA Chaperone
B: Repressor of competence, RNA Chaperone


Theoretical massNumber of molelcules
Total (without water)24,1782
Polymers24,1782
Non-polymers00
Water6,539363
1
A: Repressor of competence, RNA Chaperone


Theoretical massNumber of molelcules
Total (without water)12,0891
Polymers12,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Repressor of competence, RNA Chaperone


Theoretical massNumber of molelcules
Total (without water)12,0891
Polymers12,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.559, 81.772, 49.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-351-

HOH

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Components

#1: Protein Repressor of competence, RNA Chaperone


Mass: 12088.995 Da / Num. of mol.: 2 / Fragment: ProQ/FinO-domain, UNP residues 24-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3926_00530, DIZ73_10055 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A128QHZ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium Acetate, 0.1M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13499 / % possible obs: 97.9 % / Redundancy: 36.5 % / Biso Wilson estimate: 21.14 Å2 / CC1/2: 1 / Net I/σ(I): 35.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 28.7 % / Num. unique obs: 619 / CC1/2: 0.952 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-2000data scaling
HKL-2000data processing
Cootmodel building
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DVO, 3MW6

1dvo

3mw6


Resolution: 2.1→49.42 Å / SU ML: 0.2489 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 601 4.57 %
Rwork0.1607 12563 -
obs0.1642 13164 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 363 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611753
X-RAY DIFFRACTIONf_angle_d0.74042370
X-RAY DIFFRACTIONf_chiral_restr0.0463270
X-RAY DIFFRACTIONf_plane_restr0.004312
X-RAY DIFFRACTIONf_dihedral_angle_d13.2428682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.24441470.15863049X-RAY DIFFRACTION95.55
2.31-2.650.29281520.18363131X-RAY DIFFRACTION97.04
2.65-3.330.26241450.18493029X-RAY DIFFRACTION93.35
3.33-49.420.20121570.14113354X-RAY DIFFRACTION98.49
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)
12.490391077031.75061048855-0.5444173627093.12418520025-0.9739901365751.093686836080.04770305906080.226739424155-0.100482945425-0.0824677472235-0.0359538652712-0.1471921430740.1429641191150.136052177713-0.01450866958760.1724714917590.03188886117870.005962400592040.161306758449-0.0004611696850370.13871825008638.070718872912.670578959350.4663607739
25.434141534423.41686112862-0.6483162370778.26494563556-0.2158564725774.77245511017-0.2737770878091.03946802247-0.545582875514-1.251770341790.26595266045-0.476869800540.4883322369690.2302414899240.01407544988960.3338416657570.0466373015220.02551102790130.414247647155-0.06676479595030.20488712281236.46606044089.6895343445737.4745663568
33.69012614643.088729861913.466937048417.948852818965.219854037545.556023983530.07086302022290.3282664671240.3241878087570.118261763044-0.1777107494280.4359253964580.375677788341-0.09024005775850.1195973364540.144023163928-0.007660397748710.02707651857310.2070027452850.02413033078940.16309166703231.718332619318.23108786147.6446504603
42.967128592672.656432080341.114884002759.24337730369-0.09777170849220.8116569409270.1117462773870.128144356310.197657338717-0.256257159688-0.0664567511217-0.282473675364-0.0497649170499-0.0731090274592-0.06255035112680.1414090879970.02902144786770.04705310537430.1591258990060.03117804952760.13175065885946.394814694325.96735243446.151210521
57.122283473194.53361752014-5.763852498164.5699997214-4.44942773815.183852085170.6953408206040.421960868231.193881449570.3934655968250.2510256620150.593706718578-1.03182125244-0.819842979972-0.9172824176860.3568233706920.1031156512860.06361367541360.2617600377140.02661673124810.41606547489932.580931943934.668292625752.775263274
63.92785454332-4.05666575779-1.88821374679.013163229563.929648674043.404351421850.3300151905130.713972490541-0.272925474676-1.04922947235-0.300447626331-0.6533204425470.5356781511570.7092603539980.001870813151590.420752526090.07468326714250.09653039095840.3621744846410.1055308704770.44185695579148.13606321739.3662501432654.3069500532
74.602561922890.272426413623-0.3005200230012.57916295693-0.5668673993561.816550348920.018471655534-0.0571647996483-0.2419076445390.1001230534250.08724039231790.08239658469570.07902093172660.0369038387675-0.09324186310550.152590829366-0.0130593953296-0.01480886529640.07616885398270.01472096762930.13434627286433.48376751249.3436938739763.4200560868
87.70803252095-4.0758815805-5.151747964697.427927980253.616297994757.99337502131-0.0731592371211-0.829266957901-0.7799925045420.7548546088510.214083924542-0.2790748456380.6590201973910.37996559973-0.09577268204930.337840441514-0.0251658933157-0.09675905257170.2140735721730.06576335938160.28125556841540.64644338091.8049907909672.2293931844
94.45468681939-3.487739750230.6466034936187.24019299076-1.022417488081.83851478241-0.03838947765370.05013049940550.4344301987340.552021461266-0.123870715554-0.638298013261-0.2624206256330.2778529759840.1632177026630.176142170415-0.0419255902681-0.01853768584990.1313331835630.03117456506660.18202819965740.108300340914.868844587567.504156584
103.56844532495-0.510568092674-0.663776258880.5872670257230.156143825782.256154213780.217353706359-0.2060434694460.4988763584980.844839869666-0.04754331226910.620493852476-0.568261190881-0.203675225106-0.1322307037590.3690208767140.03411669567360.1024440107580.208328366456-0.003882732506540.26073365843427.395715550621.590818664270.8757131645
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 52 )AA19 - 521 - 34
22chain 'A' and (resid 53 through 67 )AA53 - 6735 - 49
33chain 'A' and (resid 68 through 90 )AA68 - 9050 - 73
44chain 'A' and (resid 91 through 109 )AA91 - 10974 - 93
55chain 'A' and (resid 110 through 125 )AA110 - 12594 - 110
66chain 'B' and (resid 19 through 26 )BB19 - 261 - 8
77chain 'B' and (resid 27 through 52 )BB27 - 529 - 35
88chain 'B' and (resid 53 through 67 )BB53 - 6736 - 51
99chain 'B' and (resid 68 through 90 )BB68 - 9052 - 75
1010chain 'B' and (resid 91 through 125 )BB91 - 12576 - 111

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