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- PDB-3bk2: Crystal Structure Analysis of the RNase J/UMP complex -

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Basic information

Entry
Database: PDB / ID: 3bk2
TitleCrystal Structure Analysis of the RNase J/UMP complex
ComponentsMetal dependent hydrolase
KeywordsHYDROLASE / RNase J / Endoribonuclease / Exoribonuclease / Metal dependent hydrolase / Metallo-beta-lactamase
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain ...Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Sugar transport proteins signature 1. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Ribonuclease J
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde la Sierra-Gallay, I.L. / Zig, L. / Putzer, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural insights into the dual activity of RNase J
Authors: de la Sierra-Gallay, I.L. / Zig, L. / Jamalli, A. / Putzer, H.
History
DepositionDec 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 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_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1338
Polymers63,3061
Non-polymers8277
Water3,153175
1
A: Metal dependent hydrolase
hetero molecules

A: Metal dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,26716
Polymers126,6122
Non-polymers1,65514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.080, 118.000, 228.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-993-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metal dependent hydrolase / RNase J


Mass: 63305.957 Da / Num. of mol.: 1 / Fragment: UNP residues 20-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TTC0775 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q72JJ7, Hydrolases

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, The RNase J/UMP complex was obtained by soaking of a native RNase J crystal in 100mM UMP, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 38744 / Num. obs: 38615 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.97 / Num. unique all: 4991 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BK1

3bk1


Resolution: 2.1→50 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3869 10 %RANDOM
Rwork0.217 ---
all0.227 38744 --
obs0.227 38615 99.7 %-
Solvent computationBsol: 55.659 Å2
Displacement parametersBiso mean: 41.961 Å2
Baniso -1Baniso -2Baniso -3
1-14.357 Å20 Å20 Å2
2---18.111 Å20 Å2
3---3.754 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 46 175 4525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.315
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.357 625 -
Rwork0.343 --
obs-6361 99.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3ligand_xplor_par.txt
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5water_rep.param

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