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- PDB-4pef: Dbr1 in complex with sulfate -

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Basic information

Entry
Database: PDB / ID: 4pef
TitleDbr1 in complex with sulfate
ComponentsRNA lariat debranching enzyme, putative
KeywordsHYDROLASE / NUCLEASE / PHOSPHODIESTERASE / METALLOHYDROLASE / METALLOPHOSPHOESTERASE / LARIAT RNA / METALLOENZYME
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 / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMontemayor, E.J. / Katolik, A. / Clark, N.E. / Taylor, A.B. / Schuermann, J.P. / Combs, D.J. / Johnsson, R. / Holloway, S.P. / Stevens, S.W. / Damha, M.J. / Hart, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1.
Authors: Montemayor, E.J. / Katolik, A. / Clark, N.E. / Taylor, A.B. / Schuermann, J.P. / Combs, D.J. / Johnsson, R. / Holloway, S.P. / Stevens, S.W. / Damha, M.J. / Hart, P.J.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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_asym_id / _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_asym_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)211,08223
Polymers209,5705
Non-polymers1,51218
Water19,8891104
1
A: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2535
Polymers41,9141
Non-polymers3394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2535
Polymers41,9141
Non-polymers3394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1614
Polymers41,9141
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2535
Polymers41,9141
Non-polymers3394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1614
Polymers41,9141
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.217, 141.694, 213.216
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: 41914.004 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3)pLysS / References: UniProt: C4M1P9
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M bis-tris, 25% PEG 3350, 8.5% glycerol, 1.0 mM adenosine-2',5'-diphosphate, 2.0 mM manganese sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2863 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2863 Å / Relative weight: 1
ReflectionResolution: 1.96→47.98 Å / Num. obs: 154682 / % possible obs: 97.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 13.3
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 92

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD-derived model

Resolution: 1.96→43.183 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 7762 5.02 %random
Rwork0.1911 ---
obs0.1932 154587 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.96→43.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 73 1104 15462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814829
X-RAY DIFFRACTIONf_angle_d1.13520062
X-RAY DIFFRACTIONf_dihedral_angle_d14.4745498
X-RAY DIFFRACTIONf_chiral_restr0.082101
X-RAY DIFFRACTIONf_plane_restr0.0052516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98230.37472100.31173799X-RAY DIFFRACTION76
1.9823-2.00560.34732680.27854738X-RAY DIFFRACTION96
2.0056-2.03010.33242880.25824824X-RAY DIFFRACTION96
2.0301-2.05580.30482500.24874795X-RAY DIFFRACTION96
2.0558-2.08280.29732620.23954812X-RAY DIFFRACTION96
2.0828-2.11130.27362510.23764826X-RAY DIFFRACTION97
2.1113-2.14150.3152540.23394828X-RAY DIFFRACTION97
2.1415-2.17350.28332390.23034879X-RAY DIFFRACTION97
2.1735-2.20740.27582250.21894874X-RAY DIFFRACTION97
2.2074-2.24360.26412840.21514828X-RAY DIFFRACTION97
2.2436-2.28230.27282460.21224908X-RAY DIFFRACTION97
2.2823-2.32380.27932590.21284838X-RAY DIFFRACTION97
2.3238-2.36850.25822690.21164895X-RAY DIFFRACTION97
2.3685-2.41680.25642460.20874898X-RAY DIFFRACTION98
2.4168-2.46940.28922740.21854858X-RAY DIFFRACTION98
2.4694-2.52680.26472450.21664959X-RAY DIFFRACTION98
2.5268-2.590.23252660.19854899X-RAY DIFFRACTION98
2.59-2.660.23362550.20034937X-RAY DIFFRACTION98
2.66-2.73830.26592410.21234937X-RAY DIFFRACTION98
2.7383-2.82670.25812850.20714949X-RAY DIFFRACTION98
2.8267-2.92770.24472850.19764945X-RAY DIFFRACTION98
2.9277-3.04490.24852500.19374996X-RAY DIFFRACTION98
3.0449-3.18340.22022570.19844982X-RAY DIFFRACTION98
3.1834-3.35120.21592460.18754974X-RAY DIFFRACTION98
3.3512-3.5610.21752600.18364998X-RAY DIFFRACTION98
3.561-3.83580.20762620.18125024X-RAY DIFFRACTION98
3.8358-4.22150.20442800.16315035X-RAY DIFFRACTION99
4.2215-4.83170.16282720.13835071X-RAY DIFFRACTION99
4.8317-6.08470.19382510.15345171X-RAY DIFFRACTION99
6.0847-43.19350.17752820.16175348X-RAY DIFFRACTION99

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