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- PDB-3ngy: Crystal structure of RNase T (E92G mutant) -

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Basic information

Entry
Database: PDB / ID: 3ngy
TitleCrystal structure of RNase T (E92G mutant)
Components
  • Ribonuclease T
  • his tag sequence
KeywordsHYDROLASE / exoribonuclease / RNA processing / RNA maturation / protein-DNA interactions / exo-nuclease
Function / homology
Function and homology information


rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / cellular response to UV / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding ...rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / cellular response to UV / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Ribonuclease T / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation
Authors: Hsiao, Y.-Y. / Yang, C.-C. / Lin, C.L. / Lin, J.L.J. / Duh, Y. / Yuan, H.S.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Dec 28, 2011Group: Database references
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
E: his tag sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5618
Polymers103,3845
Non-polymers1773
Water6,720373
1
A: Ribonuclease T
B: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4124
Polymers51,2942
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-21 kcal/mol
Surface area17610 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3533
Polymers51,2942
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-21 kcal/mol
Surface area16760 Å2
MethodPISA
3
E: his tag sequence


Theoretical massNumber of molelcules
Total (without water)7961
Polymers7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.763, 107.718, 121.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ribonuclease T / RNase T / Exoribonuclease T


Mass: 25646.973 Da / Num. of mol.: 4 / Mutation: E92G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / ATCC 53323 / Gene: rnt / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): RIPL
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein/peptide his tag sequence


Mass: 795.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / ATCC 53323 / Gene: rnt / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): RIPL
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAIN E IS THE N-TERMINAL HIS-TAG SEQUENCE OF ONE OF THE FOUR RNASE T SUBUNITS (CHAINS A-D).

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M ammonium citrate tribase pH 7.0, 0.1M BIS-TRIS propane pH 7.0, 10mM ErCl3-6H2O, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 39447 / Num. obs: 39447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.058 / Net I/σ(I): 23.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3547 / Rsym value: 0.3 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2F96

2f96


Resolution: 2.204→27.608 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8546 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1982 5.03 %RANDOM
Rwork0.1753 37411 --
all0.1953 39393 --
obs0.1777 39393 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.096 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 84.85 Å2 / Biso mean: 27.8473 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.4044 Å20 Å2-0 Å2
2---0.1347 Å2-0 Å2
3----1.2697 Å2
Refinement stepCycle: LAST / Resolution: 2.204→27.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 3 373 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036287
X-RAY DIFFRACTIONf_angle_d0.7278520
X-RAY DIFFRACTIONf_dihedral_angle_d15.7162193
X-RAY DIFFRACTIONf_chiral_restr0.056936
X-RAY DIFFRACTIONf_plane_restr0.0031114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2042-2.25930.23791250.18432498X-RAY DIFFRACTION93
2.2593-2.32040.25951560.1852613X-RAY DIFFRACTION100
2.3204-2.38860.24041450.18742650X-RAY DIFFRACTION100
2.3886-2.46570.261490.18942679X-RAY DIFFRACTION100
2.4657-2.55380.2781440.1882666X-RAY DIFFRACTION100
2.5538-2.65590.21871340.18792653X-RAY DIFFRACTION100
2.6559-2.77670.29711420.19272654X-RAY DIFFRACTION100
2.7767-2.92290.24521560.19712674X-RAY DIFFRACTION100
2.9229-3.10580.23251330.18712673X-RAY DIFFRACTION100
3.1058-3.34530.19561370.17772691X-RAY DIFFRACTION100
3.3453-3.68120.19471490.15772689X-RAY DIFFRACTION99
3.6812-4.21230.19321370.14682717X-RAY DIFFRACTION99
4.2123-5.30090.1791320.14472732X-RAY DIFFRACTION99
5.3009-27.60970.24161430.19072822X-RAY DIFFRACTION98

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