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- PDB-4c40: The molecular recognition of kink turn structure by the L7Ae clas... -

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Basic information

Entry
Database: PDB / ID: 4c40
TitleThe molecular recognition of kink turn structure by the L7Ae class of proteins
Components5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*C)-3'
KeywordsRNA / DNA / KINK TURN
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: RNA / Year: 2013
Title: The Molecular Recognition of Kink-Turn Structure by the L7Ae Class of Proteins.
Authors: Huang, L. / Lilley, D.M.J.
History
DepositionAug 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations
Revision 1.2Nov 27, 2013Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
Non-polymers00
Water25214
1
A: 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*C)-3'

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


Theoretical massNumber of molelcules
Total (without water)12,4682
Polymers12,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_557-x,-x+y,-z+21
MethodPISA
Unit cell
Length a, b, c (Å)70.250, 70.250, 47.700
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*C)-3' / HMKT-7


Mass: 6233.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KINK TURN MOTIF / Source: (synth.) HALOARCULA MARISMORTUI (Halophile)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.7 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 4 / Details: 3.5M SODIUM FORMATE, 0.1M SODIUM ACETATE PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→37.54 Å / Num. obs: 3827 / % possible obs: 99.9 % / Observed criterion σ(I): 3.17 / Redundancy: 10.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.17 / % possible all: 100

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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 4BW0

4bw0


Resolution: 2.2→37.5 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 37.05
RfactorNum. reflection% reflection
Rfree0.26 177 5 %
Rwork0.22 --
obs-3824 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 417 0 14 431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005468
X-RAY DIFFRACTIONf_angle_d0.996730
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr0.04695
X-RAY DIFFRACTIONf_plane_restr0.00719
LS refinement shellResolution: 2.2011→37.5432 Å
RfactorNum. reflection% reflection
Rfree0.264 177 -
Rwork0.2227 3647 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -23.3345 Å / Origin y: 41.5282 Å / Origin z: 49.2951 Å
111213212223313233
T0.3984 Å2-0.0526 Å20.0308 Å2-0.2551 Å20.0544 Å2--0.2407 Å2
L0.9179 °2-0.0958 °20.1359 °2-0.0274 °2-0.0495 °2--0.0829 °2
S0.2465 Å °0.3149 Å °-0.2214 Å °0.23 Å °-0.1509 Å °-0.0435 Å °-0.4167 Å °-0.3179 Å °0.0731 Å °
Refinement TLS groupSelection details: ALL

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