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- PDB-5k71: apo Dbr1 -

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Basic information

Entry
Database: PDB / ID: 5k71
Titleapo Dbr1
ComponentsRNA lariat debranching enzyme, putative
KeywordsHYDROLASE / metalloenzyme / apo-enzyme
Function / homology
Function and homology information


RNA lariat debranching enzyme activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / RNA splicing, via transesterification reactions / mRNA splicing, via spliceosome / manganese ion binding / iron ion binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus
Similarity search - Function
Lariat debranching enzyme, N-terminal metallophosphatase domain / : / Dbr1, C-terminal domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.57 Å
AuthorsClark, N.E. / Taylor, A.B. / Hart, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures
Authors: Clark, N.E. / Katolik, A. / Roberts, K. / Taylor, A.B. / Holloway, S.P. / Schuermann, J.P. / Montemayor, E.J. / Stevens, S.W. / Fitzpatrick, P.F. / Damha, M.J. / Hart, P.J.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.journal_id_CSD
Revision 1.2Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA lariat debranching enzyme, putative
B: RNA lariat debranching enzyme, putative
C: RNA lariat debranching enzyme, putative
D: RNA lariat debranching enzyme, putative
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,60321
Polymers206,0665
Non-polymers1,53716
Water6,756375
1
A: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6946
Polymers41,2131
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4053
Polymers41,2131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.110, 142.163, 214.300
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 lariat debranching enzyme, putative


Mass: 41213.266 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4M1P9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, lithium sulfate, glycerol, bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.57→107.15 Å / Num. obs: 134191 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 2.57→2.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PEF

4pef


Resolution: 2.57→107.15 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 6717 5.01 %
Rwork0.1943 --
obs0.1967 134191 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→107.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 80 375 14740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314763
X-RAY DIFFRACTIONf_angle_d0.6419968
X-RAY DIFFRACTIONf_dihedral_angle_d17.2255457
X-RAY DIFFRACTIONf_chiral_restr0.0472092
X-RAY DIFFRACTIONf_plane_restr0.0042497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09630.44480.18552.666-0.01571.5574-0.0519-0.2442-0.04550.03780.16-0.0279-0.1755-0.2417-0.1150.28720.0627-0.05590.3746-0.01380.31570.6899-38.8382-24.0311
22.77220.16290.66522.3875-0.28641.6010.15890.08610.312-0.0352-0.12280.0023-0.00890.1581-0.04110.3148-0.0536-0.04720.31740.08370.31534.6168-68.7038-19.546
31.4407-0.2169-0.39542.52640.34061.3162-0.03270.0216-0.09950.1605-0.111-0.14340.12490.04970.14310.4075-0.0406-0.1270.26780.04010.310353.3191-88.59449.6834
42.06010.0811-1.7471.74910.41783.51410.1489-0.52740.01110.21420.08510.0351-0.23530.3398-0.17880.31-0.12110.02610.56230.00030.380141.9668-82.17-65.5289
51.7539-0.34350.72633.81-1.18793.1272-0.11970.18520.0656-0.5093-0.04090.3680.3713-0.18960.17150.3812-0.0894-0.02410.3621-0.00240.31428.1793-96.047-43.96
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 353)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 353)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 353)
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 353)
5X-RAY DIFFRACTION5(chain 'E' and resid 5 through 353)

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