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- PDB-4peg: Dbr1 in complex with guanosine-5'-monophosphate -

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Basic information

Entry
Database: PDB / ID: 4peg
TitleDbr1 in complex with guanosine-5'-monophosphate
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
GUANOSINE-5'-MONOPHOSPHATE / : / Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _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

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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)212,32522
Polymers209,5705
Non-polymers2,75517
Water19,2761070
1
A: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5205
Polymers41,9141
Non-polymers6064
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)42,5205
Polymers41,9141
Non-polymers6064
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)42,4284
Polymers41,9141
Non-polymers5143
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)42,4284
Polymers41,9141
Non-polymers5143
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)42,4284
Polymers41,9141
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.831, 141.499, 212.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#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

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Non-polymers , 5 types, 1087 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
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 guanosine-5'-monophosphate, 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: 1.2823 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: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2→47.84 Å / Num. obs: 143800 / % possible obs: 96.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.1 / % possible all: 96.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.538 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 7198 5.01 %
Rwork0.1973 --
obs0.1989 143707 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 2→42.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14293 0 162 1070 15525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414888
X-RAY DIFFRACTIONf_angle_d0.90220158
X-RAY DIFFRACTIONf_dihedral_angle_d13.925526
X-RAY DIFFRACTIONf_chiral_restr0.0632118
X-RAY DIFFRACTIONf_plane_restr0.0032510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.33692540.28754487X-RAY DIFFRACTION96
2.0227-2.04650.32682420.27834477X-RAY DIFFRACTION96
2.0465-2.07150.30872470.25884462X-RAY DIFFRACTION96
2.0715-2.09770.2832330.25094503X-RAY DIFFRACTION96
2.0977-2.12530.31412340.2374489X-RAY DIFFRACTION96
2.1253-2.15440.26692270.2394518X-RAY DIFFRACTION96
2.1544-2.18520.26412270.23114506X-RAY DIFFRACTION96
2.1852-2.21780.24612370.22994512X-RAY DIFFRACTION96
2.2178-2.25250.24982380.22944480X-RAY DIFFRACTION96
2.2525-2.28940.27012280.22924528X-RAY DIFFRACTION96
2.2894-2.32890.26812460.22944491X-RAY DIFFRACTION96
2.3289-2.37120.25462460.22514513X-RAY DIFFRACTION96
2.3712-2.41680.2792270.22264535X-RAY DIFFRACTION96
2.4168-2.46610.2442550.22494459X-RAY DIFFRACTION96
2.4661-2.51980.24222270.22014554X-RAY DIFFRACTION96
2.5198-2.57840.23862440.20944503X-RAY DIFFRACTION96
2.5784-2.64280.25672300.21214510X-RAY DIFFRACTION96
2.6428-2.71430.26252240.21954565X-RAY DIFFRACTION96
2.7143-2.79410.26262440.21324529X-RAY DIFFRACTION96
2.7941-2.88430.24842670.2054470X-RAY DIFFRACTION96
2.8843-2.98740.24142340.20984505X-RAY DIFFRACTION96
2.9874-3.10690.24362360.2084527X-RAY DIFFRACTION96
3.1069-3.24830.2212300.24528X-RAY DIFFRACTION96
3.2483-3.41950.21742320.18634548X-RAY DIFFRACTION96
3.4195-3.63360.21292200.18534586X-RAY DIFFRACTION96
3.6336-3.9140.19552740.16814542X-RAY DIFFRACTION97
3.914-4.30750.1732430.15264631X-RAY DIFFRACTION96
4.3075-4.93010.18112470.14254693X-RAY DIFFRACTION98
4.9301-6.20830.18662380.16924837X-RAY DIFFRACTION99
6.2083-42.54790.2022670.17755021X-RAY DIFFRACTION99

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