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- PDB-3tux: Crystal structure of RtcA.ATP.Mn ternary complex -

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Basic information

Entry
Database: PDB / ID: 3tux
TitleCrystal structure of RtcA.ATP.Mn ternary complex
ComponentsRNA 3'-terminal phosphate cyclase
KeywordsTRANSFERASE / Cyclization of RNA 3'-phosphate ends / cyclase family
Function / homology
Function and homology information


RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm
Similarity search - Function
RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily ...RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChakravarty, A.K. / Smith, P. / Shuman, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.
Authors: Chakravarty, A.K. / Smith, P. / Shuman, S.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _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: RNA 3'-terminal phosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1797
Polymers38,3051
Non-polymers8746
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.530, 83.060, 52.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

21A-516-

HOH

31A-649-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA 3'-terminal phosphate cyclase / RNA cyclase / RNA-3'-phosphate cyclase


Mass: 38304.527 Da / Num. of mol.: 1 / Mutation: C308S, H309N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4475, JW5688, rtcA, yhgJ, yhgK / Production host: Escherichia coli (E. coli)
References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP)

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Non-polymers , 6 types, 312 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG5000 MME, 150 mM Ammonium sulfate, 100 mM MES pH6.5, 10 mM ATP, 20 mM Manganese chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9499 Å / Relative weight: 1
ReflectionResolution: 1.85→27.31 Å / Num. all: 26303 / Num. obs: 25908 / % possible obs: 98.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.4 Å2
Reflection shellResolution: 1.85→1.95 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_833)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGD

3kgd


Resolution: 1.85→26.658 Å / SU ML: 0.51 / σ(F): 1.37 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 1311 5.06 %RANDOM
Rwork0.1853 ---
all0.1886 26398 --
obs0.1886 25886 98.06 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.839 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7921 Å2-0 Å20 Å2
2---1.9088 Å20 Å2
3---4.8571 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 51 306 2861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072621
X-RAY DIFFRACTIONf_angle_d1.1643571
X-RAY DIFFRACTIONf_dihedral_angle_d13.784952
X-RAY DIFFRACTIONf_chiral_restr0.068416
X-RAY DIFFRACTIONf_plane_restr0.005463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.92410.30741440.24792608X-RAY DIFFRACTION96
1.9241-2.01160.30121580.22712630X-RAY DIFFRACTION97
2.0116-2.11760.26871320.20642706X-RAY DIFFRACTION98
2.1176-2.25030.27161300.19292723X-RAY DIFFRACTION98
2.2503-2.42390.26841580.19442708X-RAY DIFFRACTION99
2.4239-2.66760.25591580.18822726X-RAY DIFFRACTION99
2.6676-3.05310.26831370.18642763X-RAY DIFFRACTION99
3.0531-3.84480.2051310.16292793X-RAY DIFFRACTION99
3.8448-26.66040.23761630.17232918X-RAY DIFFRACTION99

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