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- PDB-5dh7: Two divalent metal ions and conformational changes play roles in ... -

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Basic information

Entry
Database: PDB / ID: 5dh7
TitleTwo divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mn2+
Components
  • 5'-R(*GP*GP*GP*CP*GP*UP*DC*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
  • RNA (48-MER)
KeywordsRNA / ribozyme / hammerhead
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.064 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 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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_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.ptnr2_auth_asym_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*UP*DC*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,52713
Polymers21,9222
Non-polymers60411
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-60 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.309, 85.825, 103.528
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: RNA chain RNA (48-MER)


Mass: 15484.287 Da / Num. of mol.: 1 / Mutation: G12A / Source method: obtained synthetically / Details: This RNA was made by in vitro transcription / Source: (synth.) synthetic construct (others)
#2: RNA chain 5'-R(*GP*GP*GP*CP*GP*UP*DC*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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
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: 24-ID-C / Wavelength: 1.8923 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8923 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12239 / Num. obs: 12239 / % possible obs: 92.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 26.5
Reflection shellResolution: 3→3.13 Å / Redundancy: 3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 6 / % possible all: 70.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.064→40.655 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1206 9.95 %
Rwork0.2001 --
obs0.2053 12124 92.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.064→40.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1454 11 0 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011626
X-RAY DIFFRACTIONf_angle_d0.3762532
X-RAY DIFFRACTIONf_dihedral_angle_d10.115807
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 (%)
3.0644-3.1870.3362960.2661914X-RAY DIFFRACTION70
3.187-3.3320.3121270.25041139X-RAY DIFFRACTION86
3.332-3.50760.25911330.21741219X-RAY DIFFRACTION92
3.5076-3.72720.21621520.21211231X-RAY DIFFRACTION95
3.7272-4.01480.24041410.18871286X-RAY DIFFRACTION98
4.0148-4.41830.25231470.18341256X-RAY DIFFRACTION98
4.4183-5.05660.20441370.18521302X-RAY DIFFRACTION98
5.0566-6.36690.23911400.18431291X-RAY DIFFRACTION98
6.3669-40.65810.27781330.20471280X-RAY DIFFRACTION96

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