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- PDB-5fj0: Structure of the standard kink turn HmKt-7 as simple duplex in P4... -

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Basic information

Entry
Database: PDB / ID: 5fj0
TitleStructure of the standard kink turn HmKt-7 as simple duplex in P4222 space group
ComponentsHMKT-7
KeywordsRNA / KINK TURN / RNA MOTIF
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: Nucleic Acids Res. / Year: 2016
Title: A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionOct 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Jan 10, 2024Group: 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 / 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 / _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: HMKT-7
B: HMKT-7
C: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7746
Polymers18,7013
Non-polymers733
Water00
1
A: HMKT-7
B: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5164
Polymers12,4682
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HMKT-7
hetero molecules

C: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5164
Polymers12,4682
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_449-y-1,-x-1,-z+9/21
Unit cell
Length a, b, c (Å)50.504, 50.504, 144.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: RNA chain HMKT-7


Mass: 6233.833 Da / Num. of mol.: 3 / Fragment: KINK TURN MOTIF, RESIDUES 1-19 / Source method: obtained synthetically / Source: (synth.) HALOARCULA MARISMORTUI (Halophile)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 2.26 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6
Details: 0.04 M MAGNESIUM CHLORIDE 0.05 M SODIUM CACODYLATE PH 6.0 5% V/V 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 25, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→48.32 Å / Num. obs: 10187 / % possible obs: 100 % / Observed criterion σ(I): 1.3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.3 / % 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 4CS1

4cs1


Resolution: 2.2→47.692 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 37.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 490 4.8 %
Rwork0.203 --
obs0.2047 10187 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1242 3 0 1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021395
X-RAY DIFFRACTIONf_angle_d0.4182178
X-RAY DIFFRACTIONf_dihedral_angle_d12.273672
X-RAY DIFFRACTIONf_chiral_restr0.022282
X-RAY DIFFRACTIONf_plane_restr0.00357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.51840.4871910.37033098X-RAY DIFFRACTION100
2.5184-3.17290.34221400.27853206X-RAY DIFFRACTION100
3.1729-47.70330.2011590.17623393X-RAY DIFFRACTION100
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)
10.30750.1329-0.0150.19040.15460.27770.7927-0.9719-0.0826-1.2223-0.0658-0.91550.55370.5240.00251.0314-0.0737-0.01130.90240.01570.57027.2049-51.5541297.6033
21.3934-0.2241-0.18911.04151.19241.29210.4426-1.21020.61640.0333-0.04450.0371-0.0234-0.37290.00120.8104-0.24730.06080.9098-0.10440.75726.2268-40.9724307.0666
30.3431-0.1118-0.08730.2219-0.33050.6275-0.14510.05661.1843-0.19770.4436-0.3326-0.83920.94890.0120.3998-0.99880.57970.7822-0.61041.928818.6718-30.0839307.8203
40.0899-0.03310.13340.27460.45291.11120.8985-0.26670.94970.342-0.1266-0.43711.0411.30050.03781.0649-0.1020.36391.03770.00431.284323.5175-42.575299.2708
50.264-0.18980.10810.1618-0.00460.3220.8719-0.06650.9797-0.93630.3438-0.2641-0.49621.01440.00451.2207-0.15060.46530.8609-0.031.224719.6796-40.5389291.2064
60.08760.0170.05550.52630.50680.48060.78610.10151.0836-1.002-0.137-0.0434-0.76530.975-0.0040.9902-0.13780.32830.7738-0.05991.284619.2243-33.8856299.2233
70.36830.60120.06230.98820.06940.02490.1689-1.25710.53581.0916-0.3867-1.82590.3618-0.036-0.05320.7431-0.19320.18881.1468-0.32190.948913.3718-37.1238312.6555
81.36-0.30990.95130.9043-0.46550.70290.2963-0.74310.8937-0.952-0.04260.7084-1.208-0.44450.00470.8653-0.23480.09710.9446-0.16970.67952.4682-40.9918303.4971
90.31370.02150.0856-0.00620.01670.042-0.4718-0.2853-0.4927-0.2104-0.31531.44680.2485-0.0234-0.00131.0231-0.1352-0.10080.60960.17881.3058-24.665-35.2785332.7834
100.8426-0.1038-0.86530.099-0.21392.0420.24530.0882-0.1662-0.2929-0.73472.63510.96380.351-0.08641.1065-0.00880.05080.5326-0.03471.2427-16.9632-42.515332.3782
110.34620.1170.2460.36080.28180.28630.15771.33330.42070.5430.03080.2323-0.1181.23910.02680.77480.06020.19050.85680.08310.7273-3.9111-40.5136325.2385
120.22210.00210.28230.38360.28120.46030.14140.9266-0.4127-1.0363-0.28920.84890.56060.31550.00060.8112-0.07940.081.08250.20920.9185-14.086-34.8402315.1014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:11)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 12:15)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 16:19)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:5)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 6:9)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 10:13)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 14:19)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 1:5)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 6:9)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 10:14)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 15:19)

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