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- PDB-3mei: Regulatory motif from the thymidylate synthase mRNA -

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Basic information

Entry
Database: PDB / ID: 3mei
TitleRegulatory motif from the thymidylate synthase mRNA
ComponentsRNA (5'-R(*CP*CP*GP*CP*CP*GP*CP*GP*CP*CP*AP*(5BU)P*GP*CP*CP*UP*GP*UP*GP*GP*CP*GP*G)-3')
KeywordsRNA / S-turn / C-C base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.968 Å
AuthorsDibrov, S. / McLean, J. / Hermann, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA.
Authors: Dibrov, S. / McLean, J. / Hermann, T.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*GP*CP*CP*GP*CP*GP*CP*CP*AP*(5BU)P*GP*CP*CP*UP*GP*UP*GP*GP*CP*GP*G)-3')
B: RNA (5'-R(*CP*CP*GP*CP*CP*GP*CP*GP*CP*CP*AP*(5BU)P*GP*CP*CP*UP*GP*UP*GP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0027
Polymers14,8812
Non-polymers1225
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-40 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.928, 38.564, 41.985
Angle α, β, γ (deg.)90.000, 100.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7440.312 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.76 Å3/Da / Density % sol: 30.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9197 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionRedundancy: 8.5 % / Av σ(I) over netI: 15.4 / Number: 62295 / Rmerge(I) obs: 0.064 / Χ2: 1.02 / D res high: 1.96 Å / D res low: 50 Å / Num. obs: 7328 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.22509910.0541.0069.9
3.354.2299.610.0561.07810.4
2.933.3510010.06110.4
2.662.9310010.0911.00110.4
2.472.6610010.1111.01810.4
2.322.4710010.131.03510.3
2.212.3210010.1491.0589
2.112.2198.710.13715.4
2.032.1198.910.1420.9154.9
1.962.0381.910.1541.0762.7
ReflectionResolution: 1.96→50 Å / Num. obs: 13933 / % possible obs: 97.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.021 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.96-2.032.70.1546181.076181.9
2.03-2.114.90.1427170.915198.9
2.11-2.215.40.1377361198.7
2.21-2.3290.1497461.0581100
2.32-2.4710.30.137431.0351100
2.47-2.6610.40.1117331.0181100
2.66-2.9310.40.0917511.0011100
2.93-3.3510.40.0675311100
3.35-4.2210.40.0567561.078199.6
4.22-509.90.0547751.006199

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Phasing

PhasingMethod: SAD
Phasing dm shellResolution: 2→50 Å / Delta phi final: 0.26 / FOM : 0.295 / Reflection: 13381

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.968→28.197 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.805 / SU ML: 0.3 / σ(F): 1.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.238 640 4.59 %RANDOM
Rwork0.176 ---
obs0.179 13933 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.828 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 80.09 Å2 / Biso mean: 33.136 Å2 / Biso min: 24.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.477 Å20 Å20.31 Å2
2--0.743 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.968→28.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 974 5 132 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151084
X-RAY DIFFRACTIONf_angle_d2.281688
X-RAY DIFFRACTIONf_chiral_restr0.101226
X-RAY DIFFRACTIONf_plane_restr0.01146
X-RAY DIFFRACTIONf_dihedral_angle_d16.715456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.968-2.120.3441160.2312342245885.7
2.12-2.3330.2371280.2212728285699.2
2.333-2.6710.3061300.20827482878100
2.671-3.3640.251190.1682760287999.69
3.364-28.20.1841470.152715286299.1
Refinement TLS params.Method: refined / Origin x: 6.6207 Å / Origin y: -1.5441 Å / Origin z: 52.1066 Å
111213212223313233
T0.2264 Å20.0092 Å2-0.0264 Å2-0.2542 Å2-0.0077 Å2--0.2018 Å2
L0.1938 °2-0.015 °20.0823 °2--0.1092 °20.0634 °2--0.4878 °2
S0.0066 Å °-0.0451 Å °0.1938 Å °-0.0182 Å °0.1467 Å °-0.0022 Å °0.1192 Å °-0.0055 Å °-0.1084 Å °
Refinement TLS groupSelection details: ALL

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