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- PDB-7ug9: Crystal structure of RNase AM PHP domain -

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Basic information

Entry
Database: PDB / ID: 7ug9
TitleCrystal structure of RNase AM PHP domain
Components5'-3' exoribonuclease
KeywordsHYDROLASE / FAD / 3'-FADP / RNA / cap / decapping
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / transferase activity / hydrolase activity
Similarity search - Function
PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like
Similarity search - Domain/homology
: / 5'-3' exoribonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsDoamekpor, S.K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)R35GM118093 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Identification of a novel deFADding activity in human, yeast and bacterial 5' to 3' exoribonucleases.
Authors: Sharma, S. / Yang, J. / Doamekpor, S.K. / Grudizen-Nogalska, E. / Tong, L. / Kiledjian, M.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 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 1.2Oct 18, 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: 5'-3' exoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8855
Polymers32,6241
Non-polymers2614
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.289, 74.389, 40.079
Angle α, β, γ (deg.)90.000, 118.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-3' exoribonuclease / Histidinol phosphatase and related hydrolases of the PHP family / PHP domain protein / Phosphatase ...Histidinol phosphatase and related hydrolases of the PHP family / PHP domain protein / Phosphatase / Protein TrpH / Putative enzymes / Putative phosphoesterase / S-adenosylmethionine tRNA ribosyltransferase


Mass: 32623.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yciV, trpH / Production host: Escherichia coli (E. coli)
References: UniProt: J7Q776, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG8000, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→37.19 Å / Num. obs: 42453 / % possible obs: 92.7 % / Redundancy: 2.689 % / Biso Wilson estimate: 20.42 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.139 / Χ2: 1.129 / Net I/σ(I): 6.59 / Num. measured all: 114177 / Scaling rejects: 546
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.732.6450.5822.217832339429610.7690.72887.2
1.73-1.782.6170.4842.667706325329450.8150.60890.5
1.78-1.832.6220.3943.297668326429250.8580.49589.6
1.83-1.892.5820.3323.737169309627770.8730.41889.7
1.89-1.952.5020.2614.456750302226980.9180.33189.3
1.95-2.022.4610.225.186467291926280.9050.27890
2.02-2.12.7210.1986.117059277525940.9390.24693.5
2.1-2.182.7680.176.797112273325690.9550.2194
2.18-2.282.7440.1517.166760263024640.9640.18893.7
2.28-2.392.790.147.786543248523450.9620.17394.4
2.39-2.522.7510.1218.346192236722510.9650.1595.1
2.52-2.672.6990.1138.725744223721280.9620.1495.1
2.67-2.862.5060.0998.584887209919500.970.12492.9
2.86-3.092.8410.0969.735386195718960.9760.11796.9
3.09-3.382.9280.09110.315191182617730.9710.11197.1
3.38-3.782.9020.09210.684515159515560.9670.11297.6
3.78-4.362.8570.09610.934042143914150.9640.11798.3
4.36-5.342.6920.09310.613150122411700.9690.11595.6
5.34-7.562.8450.09610.8925469318950.9680.11896.1
7.56-37.192.8420.11411.1414585345130.9630.1496.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.31 Å37.19 Å
Translation3.31 Å37.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YB1

2yb1


Resolution: 1.69→37.19 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2023 8.93 %
Rwork0.1819 20628 -
obs0.1848 22651 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.29 Å2 / Biso mean: 23.3028 Å2 / Biso min: 12.18 Å2
Refinement stepCycle: final / Resolution: 1.69→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 8 129 1760
Biso mean--18.68 31.06 -
Num. residues----206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.730.39371490.36951394154393
1.73-1.780.38391310.30781442157397
1.78-1.830.3161440.26211473161797
1.83-1.890.26931490.24591445159497
1.89-1.960.27091370.21961469160697
1.96-2.040.25271440.20591449159397
2.04-2.130.24251350.18581484161998
2.13-2.240.21381510.16421493164499
2.24-2.380.22321450.17161480162598
2.38-2.570.19751570.16621479163699
2.57-2.820.19881480.18141478162698
2.82-3.230.21851320.1741494162699
3.23-4.070.16641550.15561524167999
4.07-37.190.18771460.15781524167099

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