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- PDB-4gcw: Crystal structure of RNase Z in complex with precursor tRNA(Thr) -

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Basic information

Entry
Database: PDB / ID: 4gcw
TitleCrystal structure of RNase Z in complex with precursor tRNA(Thr)
Components
  • Ribonuclease Z
  • TRNA(THR)
KeywordsHYDROLASE/RNA / ZINC-DEPENDENT METALO BETALACTAMASE - RNA COMPLEX / TRNA MATURASE / PROTEIN-RNA COMPLEX / TRNA BINDING / HYDROLASE-RNA complex
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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonuclease Z
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPellegrini, O. / Li de la Sierra-Gallay, I. / Piton, J. / Gilet, L. / Condon, C.
CitationJournal: Structure / Year: 2012
Title: Activation of tRNA Maturation by Downstream Uracil Residues in B. subtilis
Authors: Pellegrini, O. / Li de la Sierra-Gallay, I. / Piton, J. / Gilet, L. / Condon, C.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease Z
B: TRNA(THR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5565
Polymers60,2302
Non-polymers3263
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-66 kcal/mol
Surface area22400 Å2
MethodPISA
2
B: TRNA(THR)

A: Ribonuclease Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5565
Polymers60,2302
Non-polymers3263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2070 Å2
ΔGint-91 kcal/mol
Surface area23560 Å2
MethodPISA
3
A: Ribonuclease Z
B: TRNA(THR)
hetero molecules

A: Ribonuclease Z
B: TRNA(THR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11310
Polymers120,4614
Non-polymers6526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12210 Å2
ΔGint-216 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.080, 42.550, 110.890
Angle α, β, γ (deg.)90.00, 127.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35632.594 Da / Num. of mol.: 1 / Mutation: I46M, L228M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU23840, rnz, yqjK / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P54548, tRNase Z
#2: RNA chain TRNA(THR)


Mass: 24597.713 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS SYNTHETISED AS A PRECURSOR WITH 2 NT 3'-EXTENSION. THE NT 73-76 ARE 2'-O-METHYLATED.
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG MME 2K, 0.1 M Na-MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
Details: KIRK PATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.98→43.31 Å / Num. all: 13696 / Num. obs: 13408 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 66.05 Å2 / Rsym value: 0.11 / Net I/σ(I): 10.71
Reflection shellResolution: 2.98→3.16 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.06 / Rsym value: 0.716 / % possible all: 94.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSPACKAGEdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FK6

2fk6


Resolution: 3→43.3 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.8385 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 662 5 %RANDOM
Rwork0.2269 ---
obs0.2284 13230 99.09 %-
all-13351 --
Displacement parametersBiso mean: 82.7 Å2
Baniso -1Baniso -2Baniso -3
1-31.7938 Å20 Å28.0738 Å2
2---7.4107 Å20 Å2
3----24.3831 Å2
Refine analyzeLuzzati coordinate error obs: 0.476 Å
Refinement stepCycle: LAST / Resolution: 3→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 1172 14 32 3618
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073767HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075350HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes409HARMONIC5
X-RAY DIFFRACTIONt_it3767HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3→3.24 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2763 134 5.01 %
Rwork0.2554 2543 -
all0.2564 2677 -
obs--99.09 %

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