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- PDB-5fj1: Structure of the standard kink turn HmKt-7 as stem loop in P21212... -

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Basic information

Entry
Database: PDB / ID: 5fj1
TitleStructure of the standard kink turn HmKt-7 as stem loop in P212121 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: 2.75 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 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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: HMKT-7
B: HMKT-7
C: HMKT-7
D: HMKT-7
E: HMKT-7
F: HMKT-7
G: HMKT-7
H: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,56232
Polymers62,9838
Non-polymers57924
Water28816
1
A: HMKT-7
B: HMKT-7
C: HMKT-7
E: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,92622
Polymers31,4914
Non-polymers43518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
Surface area17660 Å2
MethodPQS
2
D: HMKT-7
F: HMKT-7
G: HMKT-7
H: HMKT-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,63610
Polymers31,4914
Non-polymers1456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
Surface area17620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.052, 84.360, 174.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain
HMKT-7


Mass: 7872.823 Da / Num. of mol.: 8 / Fragment: KINK TURN MOTIF, RESIDUES 1-24 / Source method: obtained synthetically / Source: (synth.) HALOARCULA MARISMORTUI (Halophile)
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.67 Å3/Da / Density % sol: 73.68 % / Description: NONE
Crystal growpH: 7 / Details: 60% V/V TACSIMATE PH 7.0

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.75→38.72 Å / Num. obs: 32761 / % possible obs: 99.2 % / Observed criterion σ(I): 1.9 / Redundancy: 4.4 % / Biso Wilson estimate: 79.18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BW0
Resolution: 2.75→38.72 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 1626 5 %
Rwork0.1668 --
obs0.1677 32687 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.56 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4184 24 16 4224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024704
X-RAY DIFFRACTIONf_angle_d0.5757344
X-RAY DIFFRACTIONf_dihedral_angle_d11.8812272
X-RAY DIFFRACTIONf_chiral_restr0.03952
X-RAY DIFFRACTIONf_plane_restr0.005192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.83090.43781280.42052524X-RAY DIFFRACTION98
2.8309-2.92230.39111330.35322581X-RAY DIFFRACTION99
2.9223-3.02670.38941300.30872538X-RAY DIFFRACTION99
3.0267-3.14780.26531350.2692517X-RAY DIFFRACTION99
3.1478-3.2910.26991220.22282568X-RAY DIFFRACTION99
3.291-3.46440.20521140.20242582X-RAY DIFFRACTION99
3.4644-3.68130.15331660.14622536X-RAY DIFFRACTION99
3.6813-3.96530.15981470.13042592X-RAY DIFFRACTION100
3.9653-4.36380.16541640.12892580X-RAY DIFFRACTION100
4.3638-4.99410.16811310.13142627X-RAY DIFFRACTION99
4.9941-6.28770.13811360.12132654X-RAY DIFFRACTION99
6.2877-38.72390.14361200.15732762X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.95460.41010.2060.05590.01050.09620.0792-0.09570.43330.1529-0.252-0.2838-0.40620.1453-0.00020.56410.03720.00960.57960.04410.5895-4.5001-11.022420.6486
20.53050.0373-0.03060.22450.15350.08370.09571.29620.2151-0.1693-0.3381-0.74060.4592-1.2989-0.00210.67460.170.08950.99590.0880.67554.8964-11.75330.0625
30.2477-0.2434-0.11780.19830.06170.12180.64921.22790.3708-0.4772-0.3419-0.24560.44260.3378-0.00070.68340.2020.01481.07050.09830.6102-2.9794-13.8798-1.7998
40.5706-0.07070.34910.2554-0.23550.32870.71780.4186-0.4786-0.701-0.2098-0.8412-0.1434-0.70940.00160.58990.0666-0.03780.60530.15580.5505-10.8773-13.432813.0659
50.194-0.0835-0.11350.02030.06760.04580.28650.1838-0.0425-0.0234-0.0782-0.1143-0.47980.5674-0.00230.5173-0.0384-0.06290.63710.09370.55231.9531-11.701618.001
60.0957-0.11450.02070.2626-0.13290.0637-0.237-0.4798-0.2703-0.3337-0.27670.65320.76030.6085-0.00290.5504-0.023-0.00760.629-0.01060.52812.7605-24.761326.0641
70.9832-0.0571-0.04340.88630.58960.32110.3310.6863-0.34770.1048-0.35050.14850.88250.0619-0.00110.5980.1512-0.04180.7242-0.02220.6274-1.2994-32.300511.071
80.19850.2036-0.18480.2741-0.18730.13470.3312.7485-0.544-0.3105-0.07110.62030.26120.6751-00.64930.1491-0.05741.2948-0.12770.664-4.3986-30.7032-4.7142
90.3181-0.0478-0.16660.54290.44590.40690.23550.365-0.1444-0.18910.49610.07760.03190.49140.00030.60860.11340.01050.68980.00720.57866.8594-27.00098.7938
100.23560.15370.32360.40990.43680.561-0.32920.07960.01460.14480.1021-0.08840.8673-0.00320.00090.5614-0.02090.07140.582-0.09350.616-1.3191-28.300918.8185
111.01950.34490.10880.50970.74711.151-0.34861.3252-1.06630.83121.7427-0.66320.40560.94140.04450.808-0.07040.22360.69950.03541.171816.3274-47.29986.274
120.76470.01920.13570.36670.60050.9038-0.0077-0.72420.06240.3158-0.0121-0.2580.64130.6526-0.00110.61580.12470.10750.81850.16510.821719.363-33.440912.9805
130.3006-0.0940.13490.0942-0.03810.37690.2271-0.50380.7710.6831-0.51510.3937-0.19711.0857-0.00290.6885-0.0790.10130.8196-0.00310.915526.0174-16.9329.3674
141.1321-0.6281-0.0750.40550.07490.07060.3793-0.34220.4567-0.1141-0.4012-0.0444-0.00410.65210.00010.61560.02050.09520.65810.03340.743415.2293-25.79497.6978
150.34570.3515-0.44351.37070.50911.2198-0.2430.1313-0.62810.3073-0.1351-0.29340.28780.25830.00030.58920.18760.03140.639-0.03460.815718.011-38.87358.2216
160.2968-0.19720.11240.3065-0.22550.48870.20060.6850.75762.5713-0.1615-1.00010.74051.1745-0.03261.3282-0.0877-0.4181.3034-0.28641.231424.2224-1.292855.1871
170.09640.1748-0.12610.2369-0.07980.4293-0.33610.27490.6317-0.6290.5973-0.40980.20531.33820.00140.7550.0294-0.10840.926-0.26121.020917.4935-4.109141.4041
180.1355-0.0241-0.13170.3563-0.00390.1702-0.43510.5798-0.34110.330.2886-0.045-0.22870.3148-0.00060.75510.0229-0.12510.54970.01780.60012.4507-10.482533.9526
190.3496-0.71830.41661.9196-0.51980.2633-0.081-0.2125-0.38730.10490.54440.0503-0.14820.51450.00030.7253-0.0124-0.11570.7408-0.16450.633310.50182.045243.2314
200.09710.12510.06380.30780.04490.04580.3684-0.1685-0.41590.73490.3741-0.60310.60221.80270.00021.01360.2432-0.31790.9944-0.25580.971520.4457-7.785748.06
210.2493-0.36770.48750.6402-0.75890.9185-0.64810.56380.32530.35221.0808-0.7412-1.5739-0.087-0.00140.919-0.2014-0.18140.7344-0.02911.079-18.01965.53333.3962
220.61460.0355-0.01970.2593-0.45280.64030.0657-0.714-0.16920.7029-0.15150.1185-0.7271-0.7234-0.00040.66230.125-0.08810.7839-0.07990.788-21.1189-7.304311.6169
230.3804-0.02060.19360.18210.19860.30490.3916-0.519-0.1280.7119-0.6316-0.36730.249-1.1227-0.00160.7117-0.2008-0.10130.98620.1670.8281-27.9165-24.04349.8743
242.2114-1.5950.64251.2217-0.10290.75520.67980.025-0.7056-0.1692-0.7321-0.0998-0.0448-0.396600.63350.006-0.11440.6110.10750.6137-15.5086-14.01936.3572
25-0.0091-0.0446-0.01370.2427-0.19810.62790.23680.11860.73720.178-0.2480.0712-1.0042-0.23540.00020.67950.17340.03410.71090.10320.8473-22.2823-1.61167.0428
260.17950.00250.0160.0047-0.0037-0.00730.7060.4492-0.3011-1.86-0.5227-0.7782-0.27690.63260.00581.21270.01790.40771.1972-0.29191.031321.165911.887228.2015
270.0011-0.02660.01680.23660.02070.0189-0.60091.2624-1.45470.9956-0.07820.18350.04470.1627-0.00760.8253-0.15480.29880.8284-0.20660.919915.936916.637242.3765
280.22870.15220.00790.2566-0.14510.1783-0.23740.4822-0.0855-0.8521-0.19470.48430.4873-0.2257-0.00060.6718-0.11120.07590.5468-0.05420.52815.59122.022352.449
290.2632-0.34410.02590.8044-0.47720.48740.03430.32790.33-0.18430.6189-0.280.26670.3904-00.7164-0.08180.09840.7225-0.17070.55469.25979.606942.5184
300.51720.02190.42860.28430.15690.53240.52580.4346-0.1142-0.9007-0.107-0.7435-0.12250.38080.00231.1073-0.27510.2410.808-0.18920.758117.481416.46233.2855
310.10050.0686-0.01510.06270.0055-0.00420.9210.0268-0.02530.2381-0.3654-0.6557-0.34821.11330.00481.60240.2145-0.45041.3001-0.07751.221818.5718-9.17462.8339
32-0.00170.01210.02440.27460.06850.0322-0.0806-0.86480.28820.5410.41020.4283-0.06591.184-0.00381.5026-0.0253-0.10750.8986-0.07910.81384.2579-7.676462.8214
330.1616-0.057-0.03860.04270.01030.01091.1286-0.4681-2.18660.33770.69310.7095-0.6524-0.17530.0081.19780.0765-0.06690.6972-0.02911.0807-5.90831.451350.6838
340.31420.42160.13490.7662-0.00360.0476-0.13150.15680.08360.35940.42260.64450.03260.29070.00131.06550.0443-0.03920.81450.0410.8706-1.85-9.335551.7477
350.7183-0.3116-0.36260.20290.0620.25820.0214-0.6396-0.08041.09910.784-0.77970.28510.5497-0.00061.2366-0.012-0.18391.0459-0.26121.090310.5526-7.635660.0682
360.90870.8430.46891.22070.18210.32660.1806-0.8053-0.42140.70420.305-0.51420.1203-0.26290.00021.4968-0.01490.09120.91880.05970.87051.9478-26.302160.5434
370.0849-0.04310.13650.0771-0.12140.15-0.4156-0.2385-0.44910.44131.2289-1.3936-0.03070.3353-0.00171.0828-0.0290.15330.7174-0.07521.237810.5027-30.070644.8581
380.5420.28910.11570.2670.12770.1894-0.3076-0.28140.65030.6411.0148-0.28670.3437-0.40940.00071.14280.01540.10330.83140.00470.79140.149-18.757354.1815
390.4023-0.1189-0.04280.0621-0.02910.05040.5568-1.24910.29890.4456-0.3223-0.4617-0.1279-0.0970.00031.3350.11160.12320.96320.22721.0226-3.2456-25.525362.508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:7)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 8:12)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 13:16)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 17:20)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 21:24)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1:4)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 5:10)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 11:14)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 15:19)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 20:24)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 1:4)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 5:9)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 10:13)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 14:18)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 19:24)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 1:4)
17X-RAY DIFFRACTION17(CHAIN D AND RESID 5:9)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 10:13)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 14:20)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 21:24)
21X-RAY DIFFRACTION21(CHAIN E AND RESID 1:4)
22X-RAY DIFFRACTION22(CHAIN E AND RESID 5:9)
23X-RAY DIFFRACTION23(CHAIN E AND RESID 10:13)
24X-RAY DIFFRACTION24(CHAIN E AND RESID 14:19)
25X-RAY DIFFRACTION25(CHAIN E AND RESID 20:24)
26X-RAY DIFFRACTION26(CHAIN F AND RESID 2:5)
27X-RAY DIFFRACTION27(CHAIN F AND RESID 6:9)
28X-RAY DIFFRACTION28(CHAIN F AND RESID 10:13)
29X-RAY DIFFRACTION29(CHAIN F AND RESID 14:19)
30X-RAY DIFFRACTION30(CHAIN F AND RESID 20:24)
31X-RAY DIFFRACTION31(CHAIN G AND RESID 1:4)
32X-RAY DIFFRACTION32(CHAIN G AND RESID 5:8)
33X-RAY DIFFRACTION33(CHAIN G AND RESID 9:12)
34X-RAY DIFFRACTION34(CHAIN G AND RESID 13:18)
35X-RAY DIFFRACTION35(CHAIN G AND RESID 19:24)
36X-RAY DIFFRACTION36(CHAIN H AND RESID 4:10)
37X-RAY DIFFRACTION37(CHAIN H AND RESID 11:14)
38X-RAY DIFFRACTION38(CHAIN H AND RESID 15:19)
39X-RAY DIFFRACTION39(CHAIN H AND RESID 20:23)

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