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- PDB-5eaq: Two active site divalent ion in the crystal structure of the hamm... -

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Basic information

Entry
Database: PDB / ID: 5eaq
TitleTwo active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+
Components
  • RNA (48-MER)
  • RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')
KeywordsRNA / ribozyme / hammerhead
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsMir, A. / Golden, B.L.
Citation
Journal: Biochemistry / Year: 2016
Title: Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
Authors: Mir, A. / Golden, B.L.
#1: Journal: 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
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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.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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,3678
Polymers22,0372
Non-polymers3306
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-34 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.251, 87.419, 105.539
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-104-

MN

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Components

#1: RNA chain RNA (48-MER)


Mass: 15500.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
#2: RNA chain RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')


Mass: 6536.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / 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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 50 mM Tris pH 8.2, 10 mM MgCl2, 32% MPD, 0.9 M KCl, 0.5 mM spermine 2 mM NH4VO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.501 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.501 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 12773 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 139.7
Reflection shellResolution: 2.95→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 19.4 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.10_2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DI2

5di2


Resolution: 3.201→27.429 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1180 9.97 %
Rwork0.2471 --
obs0.2499 11830 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.201→27.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1456 6 0 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071628
X-RAY DIFFRACTIONf_angle_d1.2512533
X-RAY DIFFRACTIONf_dihedral_angle_d12.199795
X-RAY DIFFRACTIONf_chiral_restr0.054337
X-RAY DIFFRACTIONf_plane_restr0.00968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2009-3.34640.32691470.2831298X-RAY DIFFRACTION96
3.3464-3.52240.27471390.24751340X-RAY DIFFRACTION98
3.5224-3.74260.27711480.23051298X-RAY DIFFRACTION99
3.7426-4.03080.30781570.22281338X-RAY DIFFRACTION99
4.0308-4.43490.31481420.21681344X-RAY DIFFRACTION100
4.4349-5.07310.26131490.23091349X-RAY DIFFRACTION100
5.0731-6.37830.25671490.25821334X-RAY DIFFRACTION100
6.3783-27.430.2681490.26321349X-RAY DIFFRACTION99

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