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

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Basic information

Entry
Database: PDB / ID: 9bzc
TitleCocrystal structure of Clostridium beijerinckii ZTP riboswitch with ZMP and Cs
ComponentsRNA (87-MER)
KeywordsRNA / riboswitch / single-stranded RNA / ZMP / ZTP / AICAR
Function / homologyAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / : / : / : / RNA / RNA (> 10)
Function and homology information
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
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 ZMP and Cs
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 (87-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,57713
Polymers28,6511
Non-polymers92612
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.864, 47.673, 74.110
Angle α, β, γ (deg.)90.00, 129.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (87-MER)


Mass: 28651.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
References: GenBank: 1995533340

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Non-polymers , 5 types, 23 molecules

#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N4O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.4 %
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: APS / Beamline: 24-ID-C / Wavelength: 1.4938 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4938 Å / Relative weight: 1
ReflectionResolution: 2.52→49.86 Å / Num. obs: 17648 / % possible obs: 97.21 % / Redundancy: 3.5 % / CC1/2: 0.985 / Net I/σ(I): 9.1
Reflection shellResolution: 2.52→2.62 Å / Num. unique obs: 1756 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
AutoSolphasing
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.52→49.86 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1736 9.99 %
Rwork0.1952 --
obs0.1983 17386 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1842 33 11 1886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052083
X-RAY DIFFRACTIONf_angle_d0.9483242
X-RAY DIFFRACTIONf_dihedral_angle_d14.8381037
X-RAY DIFFRACTIONf_chiral_restr0.043437
X-RAY DIFFRACTIONf_plane_restr0.00788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.590.40141470.39841292X-RAY DIFFRACTION97
2.59-2.680.3851440.36471326X-RAY DIFFRACTION98
2.68-2.770.3871420.35781321X-RAY DIFFRACTION97
2.77-2.880.55311440.43461286X-RAY DIFFRACTION97
2.88-3.020.3581400.26181314X-RAY DIFFRACTION98
3.02-3.170.19561550.2021323X-RAY DIFFRACTION98
3.18-3.370.29221450.18651310X-RAY DIFFRACTION97
3.37-3.630.27121420.19731285X-RAY DIFFRACTION96
3.63-40.20421460.1641292X-RAY DIFFRACTION97
4-4.580.19271430.17531301X-RAY DIFFRACTION96
4.58-5.760.16141420.16741277X-RAY DIFFRACTION96
5.77-49.860.18161460.16341323X-RAY DIFFRACTION98
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)
12.2451-0.28660.54543.3070.59463.22390.05540.23170.0606-0.69090.0844-0.1754-0.1011-0.1997-0.16960.4672-0.03320.01710.51260.04950.5699-79.367354.0829128.3185
23.52410.26213.74012.3905-1.21245.74940.20860.0009-0.19660.297-0.6543-0.1855-0.20870.90450.36470.71270.1519-0.09681.09710.12510.9343-85.000787.3134105.2905
34.1423-1.94130.60961.15261.05058.20410.09810.02420.2645-0.2634-0.1618-0.2953-0.59510.06690.07340.5233-0.0249-0.02740.51440.0680.8244-82.889461.0241137.6033
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 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 89 )

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