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- PDB-3zd4: Full-Length Hammerhead Ribozyme with G12A substitution at the gen... -

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Basic information

Entry
Database: PDB / ID: 3zd4
TitleFull-Length Hammerhead Ribozyme with G12A substitution at the general base position
Components
  • HAMMERHEAD RIBOZYME, ENZYME STRAND
  • HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
KeywordsRNA / GENERAL BASE CATALYSIS
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsScott, W.G. / Schultz, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and Catalytic Effects of an Invariant Purine Substitution in the Hammerhead Ribozyme: Implications for the Mechanism of Acid-Base Catalysis.
Authors: Schultz, E.P. / Vasquez, E.E. / Scott, W.G.
History
DepositionNov 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Other
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Sep 17, 2014Group: Database references
Revision 2.0Nov 2, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / pdbx_database_status / pdbx_entity_src_syn / struct_conn / struct_ref
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAMMERHEAD RIBOZYME, ENZYME STRAND
B: HAMMERHEAD RIBOZYME, SUBSTRATE STRAND


Theoretical massNumber of molelcules
Total (without water)20,2592
Polymers20,2592
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-7.2 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.140, 68.450, 60.220
Angle α, β, γ (deg.)90.00, 112.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain HAMMERHEAD RIBOZYME, ENZYME STRAND


Mass: 13925.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: RNA chain HAMMERHEAD RIBOZYME, SUBSTRATE STRAND


Mass: 6333.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.74 % / Description: G12A MUTATED AND MODELED IN COOT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.097173
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097173 Å / Relative weight: 1
ReflectionResolution: 2.2→38.35 Å / Num. obs: 9191 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 53.23 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GOZ

2goz
PDB Unreleased entry


Resolution: 2.2→20.216 Å / SU ML: 0.33 / σ(F): 1.44 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 907 9.9 %
Rwork0.182 --
obs0.1876 9162 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→20.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1343 0 31 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051500
X-RAY DIFFRACTIONf_angle_d0.9382331
X-RAY DIFFRACTIONf_dihedral_angle_d14.735746
X-RAY DIFFRACTIONf_chiral_restr0.04311
X-RAY DIFFRACTIONf_plane_restr0.00763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33770.37441600.28451396X-RAY DIFFRACTION98
2.3377-2.51790.35051520.29331408X-RAY DIFFRACTION98
2.5179-2.77070.38941570.2841388X-RAY DIFFRACTION98
2.7707-3.17030.30751510.2331410X-RAY DIFFRACTION97
3.1703-3.98920.19171480.14871384X-RAY DIFFRACTION96
3.9892-20.21720.16591390.12831269X-RAY DIFFRACTION86
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)
15.82291.9530.04232.1739-0.4418.31540.305-0.1505-0.37760.2587-0.5892-0.08711.41820.4680.36370.59970.0597-0.04970.44420.05750.3273-9.534218.601511.6618
20.58961.21460.96856.76551.80261.4247-0.0108-0.0107-0.2627-0.57240.2107-0.942-0.11160.1653-0.25980.3042-0.00410.05820.3588-0.01990.4791-11.21777.3014-8.4746
33.38110.48052.68825.2673.6674.1046-0.6330.40470.265-0.7350.8563-0.1389-0.96380.5514-0.2880.5547-0.15950.02150.48130.05660.4111-17.754510.0028-21.1917
49.4704-2.7584-3.96348.7572-0.23528.66-1.1293-1.70060.36251.0332-0.09250.6589-0.2176-0.91271.1960.49330.028-0.06380.7181-0.18110.5702-18.22215.67950.3312
57.189-3.68084.45028.6537-1.67968.00790.0083-0.39930.2379-0.3373-0.14890.5823-0.5728-1.61940.17460.44010.107-0.16130.6258-0.08080.4785-22.827114.1219-9.8188
65.28893.6852-1.40275.8918-1.13760.3828-1.44550.07481.0929-0.53020.1727-0.3188-2.2335-1.94991.05241.13380.2002-0.37080.9593-0.08640.6167-23.530317.2769-24.8286
72.9146-2.69522.99425.7936-1.34785.47840.3934-0.0758-0.0892-0.5746-0.2651-0.0807-0.7925-0.0265-0.13760.62710.0140.01630.49990.02820.3101-31.38717.4091-32.907
83.9599-1.37782.32831.0698-0.13442.1025-0.0626-0.6905-0.08260.281-0.056-0.0049-0.3903-0.64680.12550.6249-0.0341-0.02380.71580.10840.3262-30.49512.5137-25.5497
90.0526-0.3828-0.43115.18931.5053.05830.2296-0.3693-0.28890.7241-0.2185-0.62080.78-0.664-0.04680.4593-0.0898-0.0010.41720.08250.4521-14.81692.4452-3.7866
106.44162.34630.80414.050.8019.85340.6212-0.3305-0.725-0.102-0.0247-0.6883-0.2298-0.3106-0.54220.34640.0749-0.0350.36380.02170.4943-0.343222.06999.4899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:14)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 15:25)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 26:30)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 31:34)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 35:38)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 39:43)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:7)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 8:15)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 16:20)

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