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- PDB-3tv1: Crystal structure of RtcA.AMP product complex -

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Basic information

Entry
Database: PDB / ID: 3tv1
TitleCrystal structure of RtcA.AMP product complex
ComponentsRNA 3'-terminal phosphate cyclase
KeywordsTRANSFERASE / Cyclizing 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 MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 11, 2012Group: Derived calculations
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Sep 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 / 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 / _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
B: RNA 3'-terminal phosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98312
Polymers76,6092
Non-polymers1,37410
Water13,169731
1
A: RNA 3'-terminal phosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9986
Polymers38,3051
Non-polymers6945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA 3'-terminal phosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9856
Polymers38,3051
Non-polymers6815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.160, 79.810, 85.670
Angle α, β, γ (deg.)90.00, 103.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38304.527 Da / Num. of mol.: 2 / 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 , 7 types, 741 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
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 AMP, 15 mM sodium pyrophosphate, 30 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: 1.282 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: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.9→36.91 Å / Num. all: 53820 / Num. obs: 52851 / % possible obs: 98.2 % / Biso Wilson estimate: 18.7 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGD

3kgd


Resolution: 1.9→36.907 Å / SU ML: 0.57 / σ(F): 1.35 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 2665 5.04 %RANDOM
Rwork0.18 ---
all0.1827 53834 --
obs0.1827 52827 98.13 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.87 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.334 Å20 Å21.1377 Å2
2--6.0238 Å20 Å2
3----6.3578 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 81 731 5816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075318
X-RAY DIFFRACTIONf_angle_d1.1037275
X-RAY DIFFRACTIONf_dihedral_angle_d12.9431952
X-RAY DIFFRACTIONf_chiral_restr0.067860
X-RAY DIFFRACTIONf_plane_restr0.004946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93460.25861220.20832273X-RAY DIFFRACTION85
1.9346-1.97180.2921190.19932483X-RAY DIFFRACTION93
1.9718-2.0120.26471380.18572602X-RAY DIFFRACTION97
2.012-2.05580.25771490.18562595X-RAY DIFFRACTION98
2.0558-2.10360.25291420.18382665X-RAY DIFFRACTION99
2.1036-2.15620.22891350.17312661X-RAY DIFFRACTION99
2.1562-2.21450.26761500.17782666X-RAY DIFFRACTION100
2.2145-2.27960.23131450.17392634X-RAY DIFFRACTION98
2.2796-2.35320.25681260.18412701X-RAY DIFFRACTION100
2.3532-2.43730.27641500.18862651X-RAY DIFFRACTION100
2.4373-2.53480.26521360.18222658X-RAY DIFFRACTION99
2.5348-2.65020.26341480.18782680X-RAY DIFFRACTION100
2.6502-2.78980.27461460.19842677X-RAY DIFFRACTION99
2.7898-2.96460.28111530.20492662X-RAY DIFFRACTION99
2.9646-3.19330.23131370.19812657X-RAY DIFFRACTION99
3.1933-3.51450.1991340.18172707X-RAY DIFFRACTION100
3.5145-4.02250.17421390.15962716X-RAY DIFFRACTION100
4.0225-5.06580.17881460.1422714X-RAY DIFFRACTION100
5.0658-36.9140.23391500.18932760X-RAY DIFFRACTION100

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