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- PDB-3nkb: A 1.9A crystal structure of the HDV ribozyme precleavage suggests... -

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Basic information

Entry
Database: PDB / ID: 3nkb
TitleA 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
Components
  • DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3')
  • The hepatitis delta virus ribozyme
KeywordsDNA / RNA / catalytic RNA / metal-mediated catalysis / phosphodiester cleavage
Function / homologyDNA/RNA hybrid / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.916 Å
AuthorsChen, J.-H. / Yajima, R. / Chadalavada, D.M. / Chase, E. / Bevilacqua, P.C. / Golden, B.L.
CitationJournal: Biochemistry / Year: 2010
Title: A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage.
Authors: Chen, J.H. / Yajima, R. / Chadalavada, D.M. / Chase, E. / Bevilacqua, P.C. / Golden, B.L.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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.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_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_seq_id / _struct_conn.ptnr2_label_asym_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: DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3')
B: The hepatitis delta virus ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,63612
Polymers23,3932
Non-polymers24310
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-71 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.837, 84.107, 102.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3')


Mass: 2720.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: nucleic acid was chemically synthesized
#2: RNA chain The hepatitis delta virus ribozyme


Mass: 20672.369 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Homo Sapiens (human)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 3.5 mg/mL RNA, 10 mM MgCl2, 50 mM potassium acetate, 1 mM spermine, 30% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20583 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 35.67 Å2 / Rsym value: 0.055 / Net I/σ(I): 44.3
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.423 / % possible all: 54.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CX0 WITH PORTIONS OF P2 AND P4 DELETED

1cx0
PDB Unreleased entry


Resolution: 1.916→27.361 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1994 10.05 %random
Rwork0.2141 ---
obs0.2169 19845 91.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.691 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 41.2488 Å2
Baniso -1Baniso -2Baniso -3
1-0.624 Å20 Å2-0 Å2
2--3.8266 Å20 Å2
3----4.4506 Å2
Refinement stepCycle: LAST / Resolution: 1.916→27.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1538 10 168 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031719
X-RAY DIFFRACTIONf_angle_d1.2542678
X-RAY DIFFRACTIONf_dihedral_angle_d15.206853
X-RAY DIFFRACTIONf_chiral_restr0.078357
X-RAY DIFFRACTIONf_plane_restr0.00572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.916-1.98450.31451170.29141084120157
1.9845-2.06390.29851690.25671474164376
2.0639-2.15780.29611830.26231763194690
2.1578-2.27150.2952060.26451830203695
2.2715-2.41370.2882090.25371907211697
2.4137-2.60.28832280.26581866209498
2.6-2.86140.31871960.27131957215399
2.8614-3.27480.24782030.21341984218799
3.2748-4.12360.19942340.172919692203100
4.1236-27.36330.18812490.17062017226699

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