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- PDB-3zwf: Crystal structure of Human tRNase Z, short form (ELAC1). -

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Basic information

Entry
Database: PDB / ID: 3zwf
TitleCrystal structure of Human tRNase Z, short form (ELAC1).
ComponentsZINC PHOSPHODIESTERASE ELAC PROTEIN 1
KeywordsHYDROLASE / BETA-LACTAMASE / METAL-BINDING / TRNA PROCESSING / ZINC-BINDING / CATABOLISM
Function / homology
Function and homology information


tRNase Z / tRNA-specific ribonuclease activity / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / rescue of stalled ribosome / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ribonuclease Z/BN / : / Beta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Zinc phosphodiesterase ELAC protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. ...Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of Human Trnase Z, Short Form (Elac1).
Authors: Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / ...Authors: Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
History
DepositionJul 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_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: ZINC PHOSPHODIESTERASE ELAC PROTEIN 1
B: ZINC PHOSPHODIESTERASE ELAC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,53719
Polymers81,4422
Non-polymers1,09517
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-186.8 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.520, 73.790, 73.660
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ZINC PHOSPHODIESTERASE ELAC PROTEIN 1 / DELETED IN MA29 / ELAC HOMOLOG PROTEIN 1 / RIBONUCLEASE Z 1 / RNASE Z 1 / TRNA 3 ENDONUCLEASE 1 / ...DELETED IN MA29 / ELAC HOMOLOG PROTEIN 1 / RIBONUCLEASE Z 1 / RNASE Z 1 / TRNA 3 ENDONUCLEASE 1 / TRNASE Z 1 / ELAC1


Mass: 40720.887 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 3-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9H777, tRNase Z

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Non-polymers , 5 types, 299 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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 Å3/Da / Density % sol: 38.5 % / Description: NONE
Crystal growpH: 7 / Details: 15% PEG 3350 0.2M NA NITRATE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→49.57 Å / Num. obs: 67111 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 7.82 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL DETERMINED FROM SIRAS EXPERIMENT

Resolution: 1.7→72.81 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.175 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 133-151 196-242 317-346 362-446 DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21015 3400 5.1 %RANDOM
Rwork0.18656 ---
obs0.18776 63620 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.9 Å2
2---0.24 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 55 282 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224089
X-RAY DIFFRACTIONr_bond_other_d0.0040.022703
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9635546
X-RAY DIFFRACTIONr_angle_other_deg1.2736608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55523.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7021518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214519
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02843
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free43.21252
X-RAY DIFFRACTIONr_sphericity_bonded42.79652
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 251 -
Rwork0.358 4519 -
obs--95.36 %
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)
11.17970.38850.29351.6852-0.2511.6852-0.0306-0.13550.16810.1496-0.03270.3309-0.02-0.21680.06330.35740.0182-0.22980.1274-0.02820.3728-25.78293.6157-19.0233
20.79170.39810.10972.5096-0.74580.9732-0.06510.06590.1076-0.26270.0720.34590.1079-0.1599-0.0070.3877-0.0052-0.28350.1305-0.01050.3763-26.54671.238-32.3307
30.9771-0.42570.52932.089-0.1471.4855-0.08840.01190.14460.0797-0.006-0.1959-0.09970.05080.09440.39210.0093-0.26660.0865-0.00830.3264-5.45214.2842-10.1312
40.8988-0.17140.73031.4556-0.1240.7425-0.0252-0.12470.01120.3184-0.0127-0.1468-0.02570.00130.03780.40840.0108-0.22850.11910.00880.3047-3.5865-3.89320.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION2A89 - 359
3X-RAY DIFFRACTION3B1 - 88
4X-RAY DIFFRACTION4B89 - 360

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