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- PDB-1qmi: Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiqui... -

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Basic information

Entry
Database: PDB / ID: 1qmi
TitleCrystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
ComponentsRNA 3'-TERMINAL PHOSPHATE CYCLASE
KeywordsLIGASE / 2'3'CYCLIC PHOSPHATE RNA
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
RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsPalm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of RNA 3'-Terminal Phosphate Cyclase, a Ubiquitous Enzyme with Unusual Topology
Authors: Palm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
History
DepositionSep 28, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance

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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
C: RNA 3'-TERMINAL PHOSPHATE CYCLASE
D: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)148,9954
Polymers148,9954
Non-polymers00
Water00
1
A: RNA 3'-TERMINAL PHOSPHATE CYCLASE
B: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)74,4972
Polymers74,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7.7 kcal/mol
Surface area26670 Å2
MethodPISA
2
C: RNA 3'-TERMINAL PHOSPHATE CYCLASE
D: RNA 3'-TERMINAL PHOSPHATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)74,4972
Polymers74,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-5.8 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.800, 126.600, 128.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.34768, -0.443579, -0.826049), (-0.595806, -0.575745, 0.55994), (-0.723971, 0.686845, -0.064112)195.6586, 70.0775, 116.6685
2given(0.999261, -0.034548, 0.016823), (0.034565, 0.999402, -0.000742), (-0.016787, 0.001323, 0.999858)49.3887, 0.1382, -5.1406
3given(-0.354289, -0.438311, -0.826052), (-0.572473, -0.596821, 0.562209), (-0.739428, 0.672078, -0.039474)182.37781, 37.849, 79.3294

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Components

#1: Protein
RNA 3'-TERMINAL PHOSPHATE CYCLASE / RNA CYCLASE / RNA-3'-PHOSPHATE CYCLASE


Mass: 37248.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: RTCA / Plasmid: PET11D_ECOLI CYCLASE / Cellular location (production host): CYTOPLASM / Gene (production host): RTCA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP)
Sequence detailsC-TERMINAL HIS TAG ADDED

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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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
213-15 %mPEG20001reservoir
3200 mMNa citrate1reservoir
4200 mMTris-HCl1reservoir
52 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97942
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 41596 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 7.5 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 154068
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
X-PLOR3.1phasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
Details: MODEL WAS NOT FULLY REFINED, THE HIS TAG IN CHAINS A,B,C,D WERE NOT VISIBLE IN THE ELECTRON DENSITY. THE CIS PEPTIDE GLY 232 - PRO 233 COULD ONLY BE MODELLED IN THE FULLY REFINED STRUCTURE 1QMH
RfactorNum. reflection% reflectionSelection details
Rfree0.331 1891 5 %RANDOM
Rwork0.244 ---
obs0.244 37201 89.8 %-
Displacement parametersBiso mean: 38.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9972 0 0 0 9972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS ONLY ON COORDINATES / Rms dev position: 0.48 Å / Weight position: 200
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.452 169 5 %
Rwork0.376 3342 -
obs--72 %

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