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- PDB-1y44: Crystal structure of RNase Z -

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Basic information

Entry
Database: PDB / ID: 1y44
TitleCrystal structure of RNase Z
ComponentsRibonuclease Z
KeywordsHYDROLASE / ZINC-DEPENDENT METAL HYDROLASE
Function / homology
Function and homology information


tRNase Z / 3'-tRNA processing endoribonuclease activity / zinc ion binding / identical protein binding
Similarity search - Function
Ribonuclease Z/BN / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribonuclease Z
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
Authorsde la Sierra-Gallay, I.L. / Pellegrini, O. / Condon, C.
Citation
Journal: Nature / Year: 2005
Title: Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.
Authors: de la Sierra-Gallay, I.L. / Pellegrini, O. / Condon, C.
#1: Journal: Embo J. / Year: 2003
Title: Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis
Authors: Pellegrini, O. / Nezzar, J. / Marchfelder, A. / Putzer, H. / Condon, C.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,4319
Polymers71,7342
Non-polymers6977
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-105 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.980, 188.330, 177.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribonuclease Z / RNase Z / tRNA 3 endonuclease / ZiPD / 3'tRNase / ELAC


Mass: 35867.066 Da / Num. of mol.: 2 / Mutation: I46M, L228M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rnz / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lambdaDE3 pRIL / References: UniProt: P54548, tRNase Z

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG MME 2000, ammonium sulfate, sodium-MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9766, 0.9796, 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2004 / Details: mirrors
RadiationMonochromator: 2 SILICON CRYSTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97661
20.97961
30.97971
ReflectionResolution: 2.05→50 Å / Num. obs: 85742 / Observed criterion σ(I): -3 / Redundancy: 2.32 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 0.49 / % possible all: 79.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→34.78 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2976258.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 7097 9.8 %RANDOM
Rwork0.215 ---
obs0.215 72532 89.1 %-
all-81428 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5034 Å2 / ksol: 0.380324 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å20 Å20 Å2
2--6.26 Å20 Å2
3----10.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 37 176 4614
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 1053 9.6 %
Rwork0.29 9969 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIGAND_XPLOR_TOP.TXT
X-RAY DIFFRACTION4LIGAND_XPLOR_PAR.TXTION.TOP

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