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- PDB-6h4d: Crystal structure of RsgA from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6h4d
TitleCrystal structure of RsgA from Pseudomonas aeruginosa
ComponentsSmall ribosomal subunit biogenesis GTPase RsgA
KeywordsRNA BINDING PROTEIN / CpGTPase / Ribosome maturation factor / YjeQ
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribosomal small subunit biogenesis / rRNA binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Probable gtpase engc; domain 3 / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Ribonucleotide Reductase Protein R1; domain 1 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRocchio, S. / Santorelli, D. / Travaglini-Allocatelli, C. / Federici, L. / Di Matteo, A.
CitationJournal: Febs J. / Year: 2019
Title: Structural and functional investigation of the Small Ribosomal Subunit Biogenesis GTPase A (RsgA) from Pseudomonas aeruginosa.
Authors: Rocchio, S. / Santorelli, D. / Rinaldo, S. / Franceschini, M. / Malatesta, F. / Imperi, F. / Federici, L. / Travaglini-Allocatelli, C. / Di Matteo, A.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: 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 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Small ribosomal subunit biogenesis GTPase RsgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6383
Polymers37,1291
Non-polymers5092
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-4 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.405, 146.405, 146.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Small ribosomal subunit biogenesis GTPase RsgA


Mass: 37129.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rsgA, PA4952 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HUL3, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 30% Polyacrylic acid 5100 sodium salt, 0.1 M Hepes pH 7.5, 5% PEG 200, 0.02 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→48.8 Å / Num. obs: 12464 / % possible obs: 100 % / Redundancy: 17.2 % / Biso Wilson estimate: 86.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.027 / Rrim(I) all: 0.114 / Net I/σ(I): 20.4 / Num. measured all: 214545 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0818.21.3953564919550.750.3341.4352.5100
8.7-48.815.50.04585955530.9990.0120.0476099.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rcn

2rcn


Resolution: 2.9→46.297 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 646 5.21 %
Rwork0.248 11765 -
obs0.25 12411 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.78 Å2 / Biso mean: 88.6613 Å2 / Biso min: 39.54 Å2
Refinement stepCycle: final / Resolution: 2.9→46.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 29 32 2137
Biso mean--75.31 78.83 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062145
X-RAY DIFFRACTIONf_angle_d0.9742913
X-RAY DIFFRACTIONf_chiral_restr0.039326
X-RAY DIFFRACTIONf_plane_restr0.005385
X-RAY DIFFRACTIONf_dihedral_angle_d15.501791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9004-3.12430.38821260.311222922418
3.1243-3.43860.36681360.281422842420
3.4386-3.93590.34211240.260523172441
3.9359-4.9580.28171300.22423572487
4.958-46.30320.23791300.241625152645
Refinement TLS params.Method: refined / Origin x: -14.3231 Å / Origin y: -15.5124 Å / Origin z: 15.8311 Å
111213212223313233
T0.5346 Å2-0.0646 Å2-0.0381 Å2-0.3845 Å2-0.0308 Å2--0.5306 Å2
L1.5484 °2-0.6272 °2-0.7351 °2-2.353 °20.2385 °2--2.369 °2
S0.1349 Å °-0.0787 Å °-0.2026 Å °-0.0583 Å °-0.2055 Å °0.4681 Å °0.04 Å °0.0182 Å °0.0724 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA40 - 600
2X-RAY DIFFRACTION1allZ8 - 57

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