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- PDB-4pei: Dbr1 in complex with synthetic branched RNA analog -

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Basic information

Entry
Database: PDB / ID: 4pei
TitleDbr1 in complex with synthetic branched RNA analog
Components
  • RNA (5'-R(*(G46)P*U)-3')
  • RNA (5'-R(*UP*AP*AP*CP*A)-3')
  • RNA lariat debranching enzyme, putative
KeywordsHYDROLASE/RNA / NUCLEASE / PHOSPHODIESTERASE / METALLOHYDROLASE / METALLOPHOSPHOESTERASE / LARIAT RNA / HYDROLASE / METALLOENZYME / HYDROLASE-RNA complex
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
NICKEL (II) ION / RNA / Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.2Nov 12, 2014Group: Atomic model / Derived calculations
Revision 1.3Feb 25, 2015Group: Non-polymer description
Revision 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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
V: RNA (5'-R(*UP*AP*AP*CP*A)-3')
Q: RNA (5'-R(*(G46)P*U)-3')
B: RNA lariat debranching enzyme, putative
W: RNA (5'-R(*UP*AP*AP*CP*A)-3')
R: RNA (5'-R(*(G46)P*U)-3')
C: RNA lariat debranching enzyme, putative
X: RNA (5'-R(*UP*AP*AP*CP*A)-3')
S: RNA (5'-R(*(G46)P*U)-3')
D: RNA lariat debranching enzyme, putative
Y: RNA (5'-R(*UP*AP*AP*CP*A)-3')
T: RNA (5'-R(*(G46)P*U)-3')
E: RNA lariat debranching enzyme, putative
Z: RNA (5'-R(*UP*AP*AP*CP*A)-3')
U: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,38932
Polymers216,86815
Non-polymers1,52117
Water27,5811531
1
A: RNA lariat debranching enzyme, putative
V: RNA (5'-R(*UP*AP*AP*CP*A)-3')
Q: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7137
Polymers43,3743
Non-polymers3394
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
W: RNA (5'-R(*UP*AP*AP*CP*A)-3')
R: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7236
Polymers43,3743
Non-polymers3493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
X: RNA (5'-R(*UP*AP*AP*CP*A)-3')
S: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7137
Polymers43,3743
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
Y: RNA (5'-R(*UP*AP*AP*CP*A)-3')
T: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7137
Polymers43,3743
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
Z: RNA (5'-R(*UP*AP*AP*CP*A)-3')
U: RNA (5'-R(*(G46)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5285
Polymers43,3743
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.037, 142.479, 214.665
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: 41197.199 Da / Num. of mol.: 5 / Mutation: C14S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Plasmid: YEp351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C4M1P9

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RNA chain , 2 types, 10 molecules VWXYZQRSTU

#2: RNA chain
RNA (5'-R(*UP*AP*AP*CP*A)-3')


Mass: 1554.008 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain
RNA (5'-R(*(G46)P*U)-3')


Mass: 622.479 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1548 molecules

#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1531 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.26 %
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, 2.0 mM nickel sulfate, 2.0 mM AK65

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→48.11 Å / Num. obs: 161620 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.37 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 8110 5.02 %
Rwork0.184 --
obs0.186 161552 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14277 255 79 1531 16142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415111
X-RAY DIFFRACTIONf_angle_d1.49820478
X-RAY DIFFRACTIONf_dihedral_angle_d15.6115636
X-RAY DIFFRACTIONf_chiral_restr0.1032152
X-RAY DIFFRACTIONf_plane_restr0.0072528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.32492760.28215133X-RAY DIFFRACTION100
1.9722-1.99540.32192560.25935086X-RAY DIFFRACTION100
1.9954-2.01970.28062840.24065110X-RAY DIFFRACTION100
2.0197-2.04530.28653190.23215109X-RAY DIFFRACTION100
2.0453-2.07220.27492730.23035090X-RAY DIFFRACTION100
2.0722-2.10060.28112620.22525145X-RAY DIFFRACTION100
2.1006-2.13060.27172720.21255124X-RAY DIFFRACTION100
2.1306-2.16240.27892640.21715134X-RAY DIFFRACTION100
2.1624-2.19620.27352610.21655129X-RAY DIFFRACTION100
2.1962-2.23220.2492710.20035089X-RAY DIFFRACTION100
2.2322-2.27070.26252790.20235131X-RAY DIFFRACTION100
2.2707-2.31190.27512600.20365108X-RAY DIFFRACTION100
2.3119-2.35640.24042890.19975132X-RAY DIFFRACTION100
2.3564-2.40450.2582570.19245119X-RAY DIFFRACTION100
2.4045-2.45680.24122840.20175112X-RAY DIFFRACTION99
2.4568-2.51390.2562670.19995140X-RAY DIFFRACTION99
2.5139-2.57680.24942490.19355124X-RAY DIFFRACTION99
2.5768-2.64650.23972790.19095079X-RAY DIFFRACTION99
2.6465-2.72430.24772540.19995147X-RAY DIFFRACTION99
2.7243-2.81220.24732720.19315137X-RAY DIFFRACTION99
2.8122-2.91270.23112930.18455063X-RAY DIFFRACTION98
2.9127-3.02930.26292710.18335090X-RAY DIFFRACTION98
3.0293-3.16720.22382580.1835107X-RAY DIFFRACTION98
3.1672-3.33410.20762600.17185095X-RAY DIFFRACTION98
3.3341-3.54290.20232540.16565058X-RAY DIFFRACTION97
3.5429-3.81640.2172620.16425098X-RAY DIFFRACTION97
3.8164-4.20020.17652850.15515057X-RAY DIFFRACTION97
4.2002-4.80740.17292620.13715098X-RAY DIFFRACTION97
4.8074-6.05480.18742580.15465170X-RAY DIFFRACTION97
6.0548-46.38470.19672790.17185228X-RAY DIFFRACTION94

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