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- PDB-5k73: as-isolated Dbr1 with Fe(II) and Zn(II) -

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Basic information

Entry
Database: PDB / ID: 5k73
Titleas-isolated Dbr1 with Fe(II) and Zn(II)
ComponentsRNA lariat debranching enzyme, putative
KeywordsHYDROLASE / 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
: / HYDROXIDE ION / Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)208,10334
Polymers206,0665
Non-polymers2,03629
Water10,431579
1
A: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6407
Polymers41,2131
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6407
Polymers41,2131
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6407
Polymers41,2131
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7368
Polymers41,2131
Non-polymers5237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4485
Polymers41,2131
Non-polymers2344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.161, 141.705, 213.777
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: 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) / References: UniProt: C4M1P9

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Non-polymers , 5 types, 608 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: HO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
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-C / Wavelength: 1.7316 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7316 Å / Relative weight: 1
ReflectionResolution: 2.078→70 Å / Num. obs: 223208 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.4
Reflection shellResolution: 2.08→2.17 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.5 / % possible all: 66.4

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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: 2.08→69.22 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 24.26
RfactorNum. reflection% reflection
Rfree0.2127 11177 5.01 %
Rwork0.1783 --
obs0.18 223208 86.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→69.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14294 0 85 579 14958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0414862
X-RAY DIFFRACTIONf_angle_d0.49620028
X-RAY DIFFRACTIONf_dihedral_angle_d16.0865481
X-RAY DIFFRACTIONf_chiral_restr0.0432097
X-RAY DIFFRACTIONf_plane_restr0.0032509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0777-2.10130.361470.30713017X-RAY DIFFRACTION37
2.1013-2.12610.34172310.30364245X-RAY DIFFRACTION52
2.1261-2.1520.31192650.29045234X-RAY DIFFRACTION63
2.152-2.17920.32713260.29446210X-RAY DIFFRACTION77
2.1792-2.20790.30423190.28847008X-RAY DIFFRACTION85
2.2079-2.23820.32093950.27666979X-RAY DIFFRACTION85
2.2382-2.27010.2993650.2747086X-RAY DIFFRACTION87
2.2701-2.3040.30183820.26177179X-RAY DIFFRACTION88
2.304-2.340.28874090.25397334X-RAY DIFFRACTION89
2.34-2.37840.28553910.24937319X-RAY DIFFRACTION89
2.3784-2.41940.28753290.22317126X-RAY DIFFRACTION86
2.4194-2.46340.24854500.21767383X-RAY DIFFRACTION91
2.4634-2.51080.24683920.21357583X-RAY DIFFRACTION92
2.5108-2.5620.25363770.20237551X-RAY DIFFRACTION93
2.562-2.61780.23534090.19457702X-RAY DIFFRACTION93
2.6178-2.67870.24814130.19757421X-RAY DIFFRACTION92
2.6787-2.74560.2743760.21387672X-RAY DIFFRACTION93
2.7456-2.81990.25324110.21157239X-RAY DIFFRACTION88
2.8199-2.90290.25014350.20457653X-RAY DIFFRACTION94
2.9029-2.99660.244080.19737675X-RAY DIFFRACTION94
2.9966-3.10370.24944070.19737683X-RAY DIFFRACTION94
3.1037-3.22790.22723800.19947586X-RAY DIFFRACTION93
3.2279-3.37480.23333650.18297564X-RAY DIFFRACTION92
3.3748-3.55270.21523740.17677166X-RAY DIFFRACTION87
3.5527-3.77530.19313890.15797634X-RAY DIFFRACTION93
3.7753-4.06680.17154330.14077575X-RAY DIFFRACTION93
4.0668-4.4760.14344200.1247501X-RAY DIFFRACTION92
4.476-5.12350.14814030.12367292X-RAY DIFFRACTION89
5.1235-6.45430.19013590.15277801X-RAY DIFFRACTION95
6.4543-69.25810.17124170.15217613X-RAY DIFFRACTION93
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)
11.6905-0.04390.03791.23550.12060.98360.0207-0.0934-0.0009-0.01690.03530.0116-0.1014-0.0870.05530.25550.0043-0.01060.2879-0.01310.28420.6947-38.2886-23.8151
21.29270.44110.29311.51440.02720.91210.1445-0.06750.07330.0407-0.1266-0.03980.03390.060.00550.255-0.0312-0.01520.26560.03430.252434.4967-68.3485-19.3286
30.75280.09220.01421.70040.40151.1888-0.01090.0344-0.08040.0952-0.0816-0.13450.18230.1018-0.02280.4247-0.0119-0.11170.32440.05460.368353.1694-88.2439.8283
41.20330.142-1.0780.9270.06691.93120.1224-0.2491-0.00150.05210.0083-0.0112-0.1940.2248-0.00580.2389-0.05140.03870.3319-0.00350.316241.8885-81.7603-65.1275
50.7545-0.07520.16311.6167-0.70562.0645-0.06960.05210.0539-0.1348-0.02280.16530.3308-0.28850.04430.312-0.05760.00440.3196-0.01520.30437.9435-95.584-44.0198
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 4 through 353)
5X-RAY DIFFRACTION5(chain 'E' and resid 5 through 353)

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