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- PDB-2is3: Crystal Structure of Escherichia coli RNase T -

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Basic information

Entry
Database: PDB / ID: 2is3
TitleCrystal Structure of Escherichia coli RNase T
ComponentsRibonuclease T
KeywordsHYDROLASE / RNase / ribonuclease / exoribonuclease / exonuclease / nuclease / stable RNA maturation / tRNA end-turnover
Function / homology
Function and homology information


rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response ...rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / 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 K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsZuo, Y. / Wang, Y. / Malhotra, A.
CitationJournal: Structure / Year: 2007
Title: Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover.
Authors: Zuo, Y. / Zheng, H. / Wang, Y. / Chruszcz, M. / Cymborowski, M. / Skarina, T. / Savchenko, A. / Malhotra, A. / Minor, W.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,75317
Polymers95,5044
Non-polymers1,24913
Water00
1
A: Ribonuclease T
B: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4249
Polymers47,7522
Non-polymers6727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-136 kcal/mol
Surface area16450 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3288
Polymers47,7522
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-95 kcal/mol
Surface area17800 Å2
MethodPISA
3
A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)774,020136
Polymers764,03032
Non-polymers9,991104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area108100 Å2
ΔGint-2125 kcal/mol
Surface area229390 Å2
MethodPISA
4
A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
hetero molecules

A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
hetero molecules

A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
hetero molecules

A: Ribonuclease T
B: Ribonuclease T
C: Ribonuclease T
D: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,01068
Polymers382,01516
Non-polymers4,99552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area50910 Å2
ΔGint-1063 kcal/mol
Surface area117830 Å2
MethodPISA
5
A: Ribonuclease T
B: Ribonuclease T
hetero molecules

C: Ribonuclease T
D: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,75317
Polymers95,5044
Non-polymers1,24913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
Buried area10610 Å2
ΔGint-252 kcal/mol
Surface area31570 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-246 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.140, 213.140, 149.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly of RNase T is a homodimer. The four subunits in this structure form two homodimers: chains A and B form one homodimer; chains C and D form another homodimer.

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Components

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


Mass: 23875.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: rnt / Plasmid: pUC19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4

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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: 4.43 Å3/Da / Density % sol: 72.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9786, 0.9788
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 26, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
ReflectionResolution: 3.1→30 Å / Num. obs: 31325 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 28.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→29.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 33.831 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23143 1418 5.1 %RANDOM
Rwork0.1955 ---
obs0.19735 26264 88.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 77.366 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 65 0 6104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226235
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9468465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7223.601286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48315973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4981539
X-RAY DIFFRACTIONr_chiral_restr0.0850.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024750
X-RAY DIFFRACTIONr_nbd_refined0.2360.23067
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.21
X-RAY DIFFRACTIONr_mcbond_it1.0151.53937
X-RAY DIFFRACTIONr_mcangle_it1.2226192
X-RAY DIFFRACTIONr_scbond_it1.84132544
X-RAY DIFFRACTIONr_scangle_it2.9894.52273
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 42 -
Rwork0.291 937 -
obs--43.5 %
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)
12.0262-0.29080.23273.524-1.06741.7604-0.17040.41130.3431-0.10910.0362-0.1403-0.36950.30760.1342-0.1509-0.00970.0935-0.02870.043-0.201134.304464.430734.1406
21.96890.66370.60661.20551.50376.51230.0172-0.2769-0.10350.0425-0.08640.0543-0.18650.00320.0692-0.2998-0.00470.1586-0.34670.0215-0.2159132.75451.508456.5835
33.80840.4441-0.36924.7664-1.02111.87930.07090.30830.3746-0.03020.00460.1538-0.5353-0.1348-0.0756-0.17320.05640.1254-0.0599-0.0076-0.0961105.550167.332941.9047
42.9455-1.2594-1.59891.49331.17653.0938-0.07680.341-0.3607-0.19180.05610.4172-0.0156-0.27250.0207-0.201-0.07050.0417-0.0248-0.0116-0.027785.389355.50953.3246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2097 - 209
2X-RAY DIFFRACTION2BB7 - 2117 - 211
3X-RAY DIFFRACTION3CC7 - 2097 - 209
4X-RAY DIFFRACTION4DD10 - 20910 - 209

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