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

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Basic information

Entry
Database: PDB / ID: 5eao
TitleTwo active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+
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 / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.988 Å
AuthorsMir, A. / Golden, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM095923 United States
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 20, 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 1.2Dec 25, 2019Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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_conn_type
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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)22,23210
Polymers22,0372
Non-polymers1948
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-62 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.974, 87.016, 105.370
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
11B-101-

MG

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 50 mM Tris pH 8.2, 10 mM MgCl2, 2 mM NH4VO3, 32% MPD, 0.9 M KCl, 0.5 mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9876→50 Å / Num. all: 14333 / Num. obs: 14333 / % possible obs: 94.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 51.6
Reflection shellResolution: 2.9876→3.05 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 5.7 / % possible all: 97.8

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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: 2.988→28.355 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 1405 9.87 %
Rwork0.2281 --
obs0.2323 14229 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.988→28.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1456 8 0 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041628
X-RAY DIFFRACTIONf_angle_d0.9932533
X-RAY DIFFRACTIONf_dihedral_angle_d12.069795
X-RAY DIFFRACTIONf_chiral_restr0.062337
X-RAY DIFFRACTIONf_plane_restr0.00868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9876-3.09420.35621300.30811226X-RAY DIFFRACTION94
3.0942-3.2180.32231340.23861251X-RAY DIFFRACTION98
3.218-3.36420.29151620.24911284X-RAY DIFFRACTION100
3.3642-3.54120.30221330.23021276X-RAY DIFFRACTION99
3.5412-3.76260.22961450.23211306X-RAY DIFFRACTION100
3.7626-4.05240.25421400.21421282X-RAY DIFFRACTION100
4.0524-4.45880.25791310.21271304X-RAY DIFFRACTION100
4.4588-5.10070.25961440.20081304X-RAY DIFFRACTION100
5.1007-6.41410.26461450.20621289X-RAY DIFFRACTION100
6.4141-28.35650.25391410.24411302X-RAY DIFFRACTION100

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