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- PDB-4cs1: Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg ... -

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Basic information

Entry
Database: PDB / ID: 4cs1
TitleCrystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound.
Components5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*CP)-3'
KeywordsRNA / KINK TURN / METAL ION
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: Nat.Commun. / Year: 2014
Title: A Critical Base Pair in K-Turns that Confers Folding Characteristics and Correlates with Biological Function.
Authors: Mcphee, S.A. / Huang, L. / Lilley, D.M.J.
History
DepositionMar 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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_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: 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2823
Polymers6,2341
Non-polymers492
Water41423
1
A: 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*CP)-3'
hetero molecules

A: 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5656
Polymers12,4682
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_769-x+2,-x+y+1,-z+41
MethodPISA
Unit cell
Length a, b, c (Å)70.081, 70.081, 47.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

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


Mass: 6233.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HALOARCULA MARISMORTUI (Halophile)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.53 Å3/Da / Density % sol: 51.44 % / Description: NONE
Crystal growpH: 4 / Details: 3.5 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→37.4 Å / Num. obs: 4920 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 6.3 % / Biso Wilson estimate: 42.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C40

4c40


Resolution: 2→37.415 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 225 4.6 %
Rwork0.1844 --
obs0.1866 4916 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.6 Å2
Refinement stepCycle: LAST / Resolution: 2→37.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 417 2 23 442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004468
X-RAY DIFFRACTIONf_angle_d0.805730
X-RAY DIFFRACTIONf_dihedral_angle_d12.452225
X-RAY DIFFRACTIONf_chiral_restr0.03895
X-RAY DIFFRACTIONf_plane_restr0.00719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.520.29061190.25932280X-RAY DIFFRACTION99
2.52-37.42120.21991060.16872411X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1672-1.4148-0.36352.49680.64780.16110.16630.3688-0.2482-0.55350.2658-0.5430.87620.4257-0.38311.2678-0.043-0.04980.3025-0.17920.491191.7583-55.6521100.5924
24.35412.7042-1.69246.99533.45955.58860.3349-0.27240.31850.83420.0210.051.2832-0.2298-0.28520.6174-0.168-0.00630.2838-0.03030.437887.9473-43.8944105.332
38.00212.19620.06159.0432.41182.11420.41650.42860.42140.3222-0.37210.44390.0648-0.63010.01280.3838-0.00520.030.34340.05210.410987.2042-35.550791.3152
48.2033-1.06881.75980.6572-2.1357.41070.3643-0.08160.68470.48570.2248-0.3584-0.58322.30890.09120.23260.0461-0.07120.8648-0.06820.4221103.0795-34.704392.491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:8)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:13)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 14:19)

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