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- PDB-4p43: Crystal structure of the bacterial A1408U-mutant ribosomal decodi... -

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Basic information

Entry
Database: PDB / ID: 4p43
TitleCrystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / ribosome / antibiotic-resistance / aminoglycoside / decoding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKondo, J. / Koganei, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT23790054 Japan
CitationJournal: To Be Published
Title: Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
Authors: Kondo, J. / Koganei, M.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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 / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7916
Polymers14,6652
Non-polymers1264
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-50 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 31.690, 49.410
Angle α, β, γ (deg.)90.000, 116.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Mass: 7332.368 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, MPD, Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→44.28 Å / Num. obs: 8251 / % possible obs: 99.2 % / Redundancy: 3.56 % / Rmerge(I) obs: 0.072 / Χ2: 1 / Net I/σ(I): 7.6 / Num. measured all: 29620 / Scaling rejects: 223
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2-2.073.460.3712.727888061.08397.5
2.07-2.153.630.3243.229578121.1112100
2.15-2.253.630.2923.530238311.078100
2.25-2.373.640.2523.729488091.01399.9
2.37-2.523.650.2054.430118251.041100
2.52-2.713.640.1485.330768430.926100
2.71-2.993.630.0987.429478110.886100
2.99-3.423.580.0612.130408380.93799.8
3.42-4.313.510.05414.829868350.965299.1
4.31-44.283.270.0419.828448411.059596

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXphasing
CNSrefinement
PDB_EXTRACT3.14data extraction
d*TREKdata reduction
d*TREKdata scaling
RefinementResolution: 2→44.3 Å / FOM work R set: 0.7803 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.27 878 10.6 %
Rwork0.2457 7372 -
obs-8250 99.2 %
Solvent computationBsol: 74.1715 Å2
Displacement parametersBiso max: 87.75 Å2 / Biso mean: 43.0773 Å2 / Biso min: 18.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.647 Å20 Å27.145 Å2
2---1.206 Å20 Å2
3---0.559 Å2
Refinement stepCycle: final / Resolution: 2→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 931 4 125 1060
Biso mean--38.34 47.78 -
Num. residues----44
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.786
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.5532
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.0672.5
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 (%)
2-2.070.392860.351771880497.5
2.07-2.150.2915810.3131730811100
2.15-2.250.3142930.3025739832100
2.25-2.370.306970.284671381099.9
2.37-2.520.2995970.2807728825100
2.52-2.710.2697930.2797750843100
2.71-2.990.3254840.2909727811100
2.99-3.420.3067850.214675383899.8
3.42-4.310.1654760.180375883499
4.31-44.30.2765860.246275684295.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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