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- PDB-9bz1: Cocrystal structure of Clostridium beijerinckii ZTP riboswitch wi... -

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Basic information

Entry
Database: PDB / ID: 9bz1
TitleCocrystal structure of Clostridium beijerinckii ZTP riboswitch with AICA
ComponentsRNA (84-MER)
KeywordsRNA / riboswitch / single-stranded RNA / ZMP / ZTP / AICAR
Function / homology5-amino-1H-imidazole-4-carboxamide / : / : / RNA / RNA (> 10)
Function and homology information
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJones, C.J. / Ferre D'Amare, A.R. / Tran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with AICA
Authors: Jones, C.P. / Tran, B. / Ferre-D'Amare, A.R.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (84-MER)
B: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,01318
Polymers57,3022
Non-polymers71116
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-80 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.069, 47.642, 113.791
Angle α, β, γ (deg.)90.00, 120.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (84-MER)


Mass: 28651.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1995533340
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-5AC / 5-amino-1H-imidazole-4-carboxamide


Mass: 126.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.8→49.06 Å / Num. obs: 25466 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2445 / CC1/2: 0.279

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.06 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 2003 7.89 %
Rwork0.2095 --
obs0.2125 25388 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3576 30 35 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064028
X-RAY DIFFRACTIONf_angle_d1.0736276
X-RAY DIFFRACTIONf_dihedral_angle_d14.6382004
X-RAY DIFFRACTIONf_chiral_restr0.047838
X-RAY DIFFRACTIONf_plane_restr0.007172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.45471390.40741590X-RAY DIFFRACTION98
2.87-2.950.36421420.36331684X-RAY DIFFRACTION98
2.95-3.030.33451430.33091592X-RAY DIFFRACTION98
3.03-3.130.29921390.27531729X-RAY DIFFRACTION100
3.13-3.240.25641460.22911669X-RAY DIFFRACTION99
3.24-3.370.2831500.21831710X-RAY DIFFRACTION100
3.37-3.530.25881480.21671643X-RAY DIFFRACTION99
3.53-3.710.23341390.20761674X-RAY DIFFRACTION99
3.71-3.950.23471340.17961713X-RAY DIFFRACTION100
3.95-4.250.23081450.16551675X-RAY DIFFRACTION100
4.25-4.680.19921460.18051660X-RAY DIFFRACTION100
4.68-5.350.20711460.17081693X-RAY DIFFRACTION99
5.35-6.740.20321520.17961692X-RAY DIFFRACTION100
6.75-49.060.25411340.19921661X-RAY DIFFRACTION99
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)
11.83560.0797-1.68351.50970.20182.39040.0756-0.17110.37530.5766-0.00020.3275-0.3280.0196-0.08570.5691-0.01480.12030.4326-0.08710.6705-101.417949.622234.9462
21.5525-0.34580.52551.3415-0.271.3505-0.08580.6386-0.0797-0.1575-0.7330.5046-0.0980.3390.65710.99740.1230.20350.92650.23241.0082-74.024414.407541.9273
31.4905-0.62910.00250.40430.04051.3853-0.04990.04010.1330.24620.02580.26570.22360.08410.01850.77770.02450.2090.5384-0.11730.8827-107.419940.679738.7266
40.0592-0.1051-0.36080.64190.30874.4531-0.21310.5860.1232-0.44530.86550.2294-0.7565-0.7928-0.19060.3743-0.1521-0.01280.72210.03271.022-113.813423.135511.7024
51.3882-0.8651-0.96311.49390.20552.5754-0.04970.2339-0.07490.01190.18950.2205-0.0527-0.1713-0.13360.2785-0.0088-0.04110.2704-0.03620.3189-97.027836.900114.2825
60.931-0.09970.50931.59341.17582.1894-0.117-0.47790.07810.12050.4576-1.38180.04890.4444-0.20260.49760.0098-0.05770.6226-0.18020.6877-128.0216-0.90846.9237
72.07560.692-0.32020.3190.611.9441-0.18910.1062-0.4733-0.13810.1390.50670.3273-0.26260.00820.5468-0.04850.00520.3748-0.0240.5735-94.442924.977610.3207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 89 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 45 )
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 65 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 89 )

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