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- PDB-3zp8: HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME -

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Basic information

Entry
Database: PDB / ID: 3zp8
TitleHIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME
Components
  • HAMMERHEAD RIBOZYME, ENZYME STRAND
  • HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
KeywordsRNA / CATALYTIC RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAnderson, M. / Schultz, E. / Martick, M. / Scott, W.G.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Active-Site Monovalent Cations Revealed in a 1.55 A Resolution Hammerhead Ribozyme Structure
Authors: Anderson, M. / Schultz, E. / Martick, M. / Scott, W.G.
History
DepositionFeb 26, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionMar 6, 2013ID: 3ZD3
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: HAMMERHEAD RIBOZYME, ENZYME STRAND
B: HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,64318
Polymers20,2752
Non-polymers36816
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-149.9 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.820, 68.530, 58.900
Angle α, β, γ (deg.)90.00, 112.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1047-

NA

21A-2026-

HOH

31A-2040-

HOH

41A-2125-

HOH

51B-2012-

HOH

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Components

#1: RNA chain HAMMERHEAD RIBOZYME, ENZYME STRAND


Mass: 13941.326 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: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE (OMC): OMC OR 2'-OMEC AT POSITION 6 OF CHAIN B

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 % / Description: SAME CELL AND SPACEGROUP AS 2GOZ
Crystal growDetails: 1.7M SODIUM MALONATE, PH 7.5 AND 1 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→20.39 Å / Num. obs: 26462 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 24.76 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.9
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.63 / % possible all: 99.6

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Processing

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

2goz
PDB Unreleased entry


Resolution: 1.55→20.39 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 2002 7.6 %
Rwork0.1867 --
obs0.1889 26446 97.48 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→20.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1344 16 289 1649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041501
X-RAY DIFFRACTIONf_angle_d0.9452333
X-RAY DIFFRACTIONf_dihedral_angle_d14.414746
X-RAY DIFFRACTIONf_chiral_restr0.041311
X-RAY DIFFRACTIONf_plane_restr0.00863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58880.35151330.31771797X-RAY DIFFRACTION100
1.5888-1.63170.29741500.28221775X-RAY DIFFRACTION99
1.6317-1.67970.29131490.25491753X-RAY DIFFRACTION99
1.6797-1.73390.2831480.24081780X-RAY DIFFRACTION100
1.7339-1.79580.27371320.22351774X-RAY DIFFRACTION100
1.7958-1.86770.27351620.22741775X-RAY DIFFRACTION100
1.8677-1.95260.24841360.23031797X-RAY DIFFRACTION100
1.9526-2.05550.25431490.21941752X-RAY DIFFRACTION100
2.0555-2.18410.24581470.21811774X-RAY DIFFRACTION99
2.1841-2.35250.24851460.21071780X-RAY DIFFRACTION99
2.3525-2.58880.24461490.21041751X-RAY DIFFRACTION98
2.5888-2.96250.21731460.2031759X-RAY DIFFRACTION98
2.9625-3.72870.18141430.14361700X-RAY DIFFRACTION95
3.7287-20.39190.16051120.14611477X-RAY DIFFRACTION80
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)
17.55893.2265-1.73238.158-5.25143.59130.1547-0.42780.0789-1.4030.23820.34181.62020.0085-0.38830.43160.0295-0.04050.34290.02970.1839-9.66318.322311.1163
21.00892.00922.45316.81147.03265.6705-0.0080.0161-0.4514-0.62920.4407-0.9951-0.35760.1767-0.44930.2428-0.02960.08910.1949-0.03720.316-11.60637.0209-8.8082
34.445-1.0146-0.9064.51932.93857.2762-0.1646-0.2022-0.0671-0.15330.2255-0.2982-0.67960.0287-0.02850.18020.0206-0.02810.19780.00030.0899-18.98019.6844-21.8264
45.7837-4.9699-2.4978.06511.86516.3432-0.2844-1.1341-0.31730.58020.21060.5471-0.5765-0.60020.19780.4081-0.01630.03850.4264-0.02320.1951-18.40715.42510.0882
56.1488-6.70117.70847.5386-8.05429.5640.0191-0.7192-0.5267-0.04730.44050.5001-0.3146-1.4248-0.48780.36370.114-0.06120.5064-0.08750.2448-23.602513.3748-9.7369
63.8332-0.45960.43544.4477-0.8280.1878-0.21220.24950.4594-0.35130.0654-0.2216-1.5225-1.26830.17460.54350.1768-0.09510.41860.00980.1993-24.771416.5656-25.3414
78.7637-4.4742-1.64417.4948-1.34611.54020.05650.3643-0.5882-0.29340.21160.37570.03510.3856-0.22820.2056-0.0074-0.02490.3301-0.03290.1159-32.77846.9324-32.8599
87.7436-4.34154.08192.4696-2.08132.3634-0.2629-0.41640.27410.18680.123-0.0495-0.02010.10510.19440.19970.0268-0.03070.3159-0.02040.1371-31.281512.1098-25.3204
94.26562.37033.49474.42984.04947.45330.0415-0.3701-0.03360.7931-0.0481-0.5409-0.2592-0.0024-0.180.35890.0152-0.050.19560.03750.2573-15.00722.2096-3.894
108.1564-3.1591-3.83937.39127.94378.84420.56-0.2079-0.3825-0.26720.2078-2.89230.46350.2495-0.5810.41220.06420.17770.2880.14840.8703-0.377421.77379.2951
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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