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- PDB-5di4: Two divalent metal ions and conformational changes play roles in ... -

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Basic information

Entry
Database: PDB / ID: 5di4
TitleTwo divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at low pH
Components
  • 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
  • RNA (48-MER)
KeywordsRNA / ribozyme / hammerhead
Function / homology: / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.948 Å
AuthorsMir, A. / Chen, J. / Neau, D. / Golden, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095923 United States
CitationJournal: Biochemistry / Year: 2015
Title: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.
Authors: Mir, A. / Chen, J. / Robinson, K. / Lendy, E. / Goodman, J. / Neau, D. / Golden, B.L.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (48-MER)
B: 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,54313
Polymers21,9382
Non-polymers60411
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-60 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.169, 85.923, 104.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-101-

MN

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Components

#1: RNA chain RNA (48-MER)


Mass: 15500.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA was made by in vitro transcription / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'


Mass: 6437.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 33 % MPD, 0.4 M potassium chloride, 50 mM potassium acetate pH 5.0, 10 mM MgCl2 and 0.5mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.5011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5011 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. all: 14606 / Num. obs: 14606 / % possible obs: 99.8 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 36.9
Reflection shellResolution: 2.94→2.99 Å / Redundancy: 37.9 % / Mean I/σ(I) obs: 7.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.948→28.215 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1446 10.02 %
Rwork0.2094 --
obs0.2118 14432 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.948→28.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1455 11 0 1466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011627
X-RAY DIFFRACTIONf_angle_d0.3882534
X-RAY DIFFRACTIONf_dihedral_angle_d10.735807
X-RAY DIFFRACTIONf_chiral_restr0.022338
X-RAY DIFFRACTIONf_plane_restr0.00268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9484-3.05370.29651360.30541255X-RAY DIFFRACTION95
3.0537-3.17580.32831420.24191268X-RAY DIFFRACTION97
3.1758-3.32010.26211520.22581292X-RAY DIFFRACTION98
3.3201-3.49480.26311350.22351290X-RAY DIFFRACTION97
3.4948-3.71330.28641500.22841298X-RAY DIFFRACTION99
3.7133-3.99930.25921400.20331325X-RAY DIFFRACTION99
3.9993-4.40040.23121590.20131296X-RAY DIFFRACTION100
4.4004-5.03410.21721480.18891329X-RAY DIFFRACTION100
5.0341-6.33050.17331390.18381317X-RAY DIFFRACTION100
6.3305-28.2160.22551450.21481316X-RAY DIFFRACTION99

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