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- PDB-2f96: 2.1 A crystal structure of Pseudomonas aeruginosa rnase T (Ribonu... -

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Basic information

Entry
Database: PDB / ID: 2f96
Title2.1 A crystal structure of Pseudomonas aeruginosa rnase T (Ribonuclease T)
ComponentsRibonuclease T
KeywordsStructural genomics / Hydrolase / RNASE / RNT / RNASE T / RIBONUCLEASE T / TRNA HYDROLASE / SAD / PSI / MCSG / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


DNA polymerase III, core complex / tRNA 3'-end processing / RNA exonuclease activity, producing 5'-phosphomonoesters / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / magnesium ion 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsZheng, H. / Chruszcz, M. / Cymborowski, M. / Wang, Y. / Gorodichtchenskaia, E. / Skarina, T. / Guthrie, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. ...Zheng, H. / Chruszcz, M. / Cymborowski, M. / Wang, Y. / Gorodichtchenskaia, E. / Skarina, T. / Guthrie, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
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
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease T
B: Ribonuclease T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2094
Polymers50,1602
Non-polymers492
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-33 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.879, 76.636, 61.666
Angle α, β, γ (deg.)90.00, 93.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: MSE / Auth seq-ID: 19 - 220 / Label seq-ID: 19 - 220

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
116AA
216BB
124AA
224BB

NCS ensembles :
ID
1
2

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Components

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


Mass: 25080.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: rnt, PA3528 / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD MAGIC (DE3)
References: UniProt: Q9HY82, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, 25% W/V, MG CHLORIDE 0.2 M BIS-TRIS 0.3M NDSB 256, , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2005 / Details: SI 111 CHANNEL
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 27229 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 17.93
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.567 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
SOLVERESOLVEphasing
ARP/wARPmodel building
Omodel building
Cootmodel building
CCP4model building
REFMAC5.2.0005refinement
HKL-3000phasing
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→19.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.999 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20448 1366 5 %RANDOM
Rwork0.15775 ---
obs0.16013 25803 99.29 %-
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: 28.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.09→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 2 230 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223173
X-RAY DIFFRACTIONr_bond_other_d0.0010.022892
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9414285
X-RAY DIFFRACTIONr_angle_other_deg0.77336668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57622.535142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28915505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2251525
X-RAY DIFFRACTIONr_chiral_restr0.080.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.2050.2580
X-RAY DIFFRACTIONr_nbd_other0.1760.22666
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21552
X-RAY DIFFRACTIONr_nbtor_other0.0850.21865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.43332146
X-RAY DIFFRACTIONr_mcbond_other0.6073829
X-RAY DIFFRACTIONr_mcangle_it3.10253161
X-RAY DIFFRACTIONr_scbond_it5.73181294
X-RAY DIFFRACTIONr_scangle_it7.618111124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Number: 2980 / Refine-ID: X-RAY DIFFRACTION

Ens-IDTypeRms dev position (Å)Weight position
2medium positional0.520.5
1loose positional0.525
2medium thermal0.882
1loose thermal0.8810
LS refinement shellResolution: 2.09→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 97 -
Rwork0.195 1749 -
obs--93.19 %
Refinement TLS params.Method: refined / Origin x: 5.289 Å / Origin y: 32.182 Å / Origin z: 42.884 Å
111213212223313233
T-0.1787 Å2-0.0071 Å2-0.0076 Å2--0.1152 Å20.0027 Å2--0.1512 Å2
L0.5065 °2-0.0595 °2-0.0011 °2-0.3493 °20.0691 °2--1.3162 °2
S0.0121 Å °-0.0014 Å °-0.0022 Å °-0.024 Å °0.0283 Å °-0.0619 Å °0.0125 Å °0.08 Å °-0.0403 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 22019 - 220
2X-RAY DIFFRACTION1BB19 - 22019 - 220

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