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- PDB-3tw3: Crystal structure of RtcA.ATP.Co ternary complex -

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Basic information

Entry
Database: PDB / ID: 3tw3
TitleCrystal structure of RtcA.ATP.Co ternary complex
ComponentsRNA 3'-terminal phosphate cyclase
KeywordsTRANSFERASE / Cyclizing 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: 2.1 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 21, 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.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.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

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Assembly

Deposited unit
A: RNA 3'-terminal phosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0856
Polymers38,3051
Non-polymers7805
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 82.950, 51.780
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-340-

CO

21A-437-

HOH

31A-466-

HOH

41A-478-

HOH

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Components

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


Mass: 38304.527 Da / Num. of mol.: 1 / Mutation: C308S and 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)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28 % PEG 5000 MME, 150 mM Ammonium sulfate, 100mM MES pH 6.5, 10 mM ATP, 20 mM Cobalt 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: 1.6051 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: 1.6051 Å / Relative weight: 1
ReflectionResolution: 2.1→32.371 Å / Num. all: 18149 / Num. obs: 17859 / % possible obs: 98.4 % / Biso Wilson estimate: 31.4 Å2
Reflection shellResolution: 2.1→2.21 Å / % possible all: 90

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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: 2.1→32.371 Å / SU ML: 0.59 / σ(F): 1.45 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 901 5.06 %RANDOM
Rwork0.2068 ---
all0.2096 18120 --
obs0.2096 17812 98.31 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.749 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.6715 Å20 Å20 Å2
2--1.9002 Å20 Å2
3---7.7713 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 39 140 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072595
X-RAY DIFFRACTIONf_angle_d0.8453532
X-RAY DIFFRACTIONf_dihedral_angle_d13.318934
X-RAY DIFFRACTIONf_chiral_restr0.054415
X-RAY DIFFRACTIONf_plane_restr0.004458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.3661290.33082557X-RAY DIFFRACTION90
2.2316-2.40380.3221600.24542791X-RAY DIFFRACTION99
2.4038-2.64560.2791650.22152798X-RAY DIFFRACTION100
2.6456-3.02820.27871420.21972861X-RAY DIFFRACTION100
3.0282-3.81430.23691370.19142889X-RAY DIFFRACTION100
3.8143-32.37480.23621680.17763015X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.9828 Å / Origin y: -7.2488 Å / Origin z: -11.8776 Å
111213212223313233
T0.1238 Å20.0194 Å2-0.0066 Å2-0.0631 Å2-0.0218 Å2--0.0022 Å2
L3.8693 °2-0.6258 °2-0.3058 °2-0.6982 °2-0.5093 °2--0.7317 °2
S-0.0006 Å °0.4519 Å °-0.2128 Å °-0.0395 Å °-0.0772 Å °0.0711 Å °0.0135 Å °0.0522 Å °-0.0477 Å °
Refinement TLS groupSelection details: all

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