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- PDB-4o8j: Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase ... -

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Basic information

Entry
Database: PDB / ID: 4o8j
TitleCrystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii, in complex with rACAAA3'phosphate and adenine.
Components
  • RNA
  • RNA 3'-terminal phosphate cyclase
KeywordsLigase/RNA / 3' RNA Cyclase / RNA / Ligase-RNA complex
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 / RNA / RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsDesai, K.K. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
CitationJournal: Rna / Year: 2014
Title: Structure of RNA 3'-phosphate cyclase bound to substrate RNA.
Authors: Desai, K.K. / Bingman, C.A. / Cheng, C.L. / Phillips Jr., G.N. / Raines, R.T.
History
DepositionDec 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Sep 23, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: RNA
E: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0277
Polymers78,2554
Non-polymers7733
Water10,989610
1
A: RNA 3'-terminal phosphate cyclase
E: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3953
Polymers39,1272
Non-polymers2671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area14000 Å2
MethodPISA
2
B: RNA 3'-terminal phosphate cyclase
D: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6334
Polymers39,1272
Non-polymers5062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-4 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.921, 110.261, 127.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37221.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1529, PHCV028, rtcA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O59198, RNA 3'-terminal-phosphate cyclase (ATP)
#2: RNA chain RNA


Mass: 1906.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M proline, 0.1 M HEPES pH 7.5, 10% PEG 3350, cryoprotected by supplementing with 30% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2013
RadiationMonochromator: Dual silicon, K-B mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 75635 / Num. obs: 75619 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 %
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O89

4o89


Resolution: 2.04→46.14 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1968 2.74 %thin shells
Rwork0.1587 ---
all0.16 71784 --
obs0.1597 71772 94.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 218 53 610 6129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125674
X-RAY DIFFRACTIONf_angle_d1.3637735
X-RAY DIFFRACTIONf_dihedral_angle_d14.9332150
X-RAY DIFFRACTIONf_chiral_restr0.082892
X-RAY DIFFRACTIONf_plane_restr0.007948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0401-2.09110.2846700.20912481X-RAY DIFFRACTION47
2.0911-2.14760.25971160.20724145X-RAY DIFFRACTION80
2.1476-2.21080.2061410.18534961X-RAY DIFFRACTION94
2.2108-2.28220.2531450.18495168X-RAY DIFFRACTION99
2.2822-2.36370.23781470.175232X-RAY DIFFRACTION100
2.3637-2.45840.22961490.15935243X-RAY DIFFRACTION100
2.4584-2.57020.22061470.15855233X-RAY DIFFRACTION100
2.5702-2.70570.20881480.15155259X-RAY DIFFRACTION100
2.7057-2.87520.18111480.15455245X-RAY DIFFRACTION100
2.8752-3.09720.17671490.15235275X-RAY DIFFRACTION100
3.0972-3.40880.21821500.14885303X-RAY DIFFRACTION100
3.4088-3.90180.17811490.14385307X-RAY DIFFRACTION100
3.9018-4.9150.16531520.13435394X-RAY DIFFRACTION100
4.915-46.15140.19021570.18255558X-RAY DIFFRACTION100

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