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- PDB-3pqv: Cyclase homolog -

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Basic information

Entry
Database: PDB / ID: 3pqv
TitleCyclase homolog
ComponentsRcl1 protein
KeywordsUNKNOWN FUNCTION / Rtc-like / cyclase-like / modular / alpha-beta / anion pocket / Ribosome Biogenesis
Function / homology
Function and homology information


endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / enzyme activator activity / RNA endonuclease activity / 90S preribosome / nucleolus
Similarity search - Function
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 type 2 / 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, 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 type 2 / 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
DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / KLLA0C05984p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.609 Å
AuthorsTanaka, N. / Smith, P. / Shuman, S.
CitationJournal: Rna / Year: 2011
Title: Crystal structure of Rcl1, an essential component of the eukaryal pre-rRNA processosome implicated in 18s rRNA biogenesis.
Authors: Tanaka, N. / Smith, P. / Shuman, S.
History
DepositionNov 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Rcl1 protein
B: Rcl1 protein
C: Rcl1 protein
D: Rcl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,44812
Polymers160,3934
Non-polymers1,0558
Water6,702372
1
A: Rcl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3543
Polymers40,0981
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rcl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3543
Polymers40,0981
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rcl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2482
Polymers40,0981
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rcl1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4914
Polymers40,0981
Non-polymers3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.317, 138.821, 228.945
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
Rcl1 protein


Mass: 40098.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0C05984g / Plasmid: pET28b-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUC5
#2: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Na Tartrate, 12.5% (w/v) PEG 3350. Cryoprotection via addition of 20% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 58656 / Num. obs: 57424 / % possible obs: 97.9 % / Observed criterion σ(I): -1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 23.83
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
2.6-2.647.50.7272.24273095.1
7.05-5012.60.03182.06320299.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.609→49.242 Å / SU ML: 0.35 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2886 5.03 %Random (CCP4 unique)
Rwork0.2043 ---
all0.21 58656 --
obs0.207 57348 97.87 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.529 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.8924 Å2-0 Å20 Å2
2---13.5253 Å2-0 Å2
3---1.6329 Å2
Refinement stepCycle: LAST / Resolution: 2.609→49.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10887 0 70 372 11329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311172
X-RAY DIFFRACTIONf_angle_d0.70415088
X-RAY DIFFRACTIONf_dihedral_angle_d12.2434219
X-RAY DIFFRACTIONf_chiral_restr0.0461731
X-RAY DIFFRACTIONf_plane_restr0.0031906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.609-2.70250.35012850.29345156X-RAY DIFFRACTION94
2.7025-2.81070.35372650.27575225X-RAY DIFFRACTION95
2.8107-2.93860.32852860.28155252X-RAY DIFFRACTION96
2.9386-3.09350.32512860.26025353X-RAY DIFFRACTION97
3.0935-3.28730.30222860.23465400X-RAY DIFFRACTION98
3.2873-3.5410.28222850.21715454X-RAY DIFFRACTION99
3.541-3.89730.23832860.19045532X-RAY DIFFRACTION100
3.8973-4.46090.22223040.16565573X-RAY DIFFRACTION100
4.4609-5.6190.21372960.16235634X-RAY DIFFRACTION100
5.619-49.25040.23733070.19485883X-RAY DIFFRACTION100

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