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- PDB-1kfo: CRYSTAL STRUCTURE OF AN RNA HELIX RECOGNIZED BY A ZINC-FINGER PRO... -

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Basic information

Entry
Database: PDB / ID: 1kfo
TitleCRYSTAL STRUCTURE OF AN RNA HELIX RECOGNIZED BY A ZINC-FINGER PROTEIN: AN 18 BASE PAIR DUPLEX AT 1.6 RESOLUTION
Components5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsLima, S. / Hildenbrand, J. / Korostelev, A. / Hattman, S. / Li, H.
CitationJournal: RNA / Year: 2002
Title: Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.
Authors: Lima, S. / Hildenbrand, J. / Korostelev, A. / Hattman, S. / Li, H.
History
DepositionNov 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 99Short contacts exhibited by residue 19 are due to the fact that residue 19 was not included in ...Short contacts exhibited by residue 19 are due to the fact that residue 19 was not included in refinement and was left unrefined.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,1321
Polymers6,1321
Non-polymers00
Water68538
1
A: 5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'

A: 5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)12,2632
Polymers12,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)45.336, 45.336, 95.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 6131.561 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMRNA1drop
250 mMcacodylate acid1droppH6.5
35 mM1dropMgCl2
42.5-5 mM1dropor CrSO4CrCl2
50.8-1.1 M1dropLiSO4
6100 mMcacodylate acid1reservoirpH6.5
75 mM1reservoirMgCl2
81.9-2.2 mM1reservoirLiSO4

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 16.5 Å2
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.056

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementResolution: 1.6→16.69 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 635784.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1346 9.8 %RANDOM
Rwork0.26 ---
obs0.26 13798 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3081 Å2 / ksol: 0.456314 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å21.92 Å20 Å2
2--2.94 Å20 Å2
3----5.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→16.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 400 1 38 439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 215 9.8 %
Rwork0.286 1968 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.211
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.317 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.286

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