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- PDB-5irf: Reverse transcriptase domain of group II intron maturase from Ros... -

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Basic information

Entry
Database: PDB / ID: 5irf
TitleReverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P1 space group
ComponentsRetron-type reverse transcriptase
KeywordsRNA BINDING PROTEIN / Group II intron / maturase / reverse transcriptase
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / defense response to virus / RNA binding
Similarity search - Function
RNA-directed DNA polymerase (reverse transcriptase), msDNA / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Retron-type reverse transcriptase
Similarity search - Component
Biological speciesRoseburia intestinalis XB6B4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhao, C. / Pyle, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM50313 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.
Authors: Zhao, C. / Pyle, A.M.
History
DepositionMar 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retron-type reverse transcriptase
B: Retron-type reverse transcriptase
C: Retron-type reverse transcriptase
D: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8298
Polymers139,6724
Non-polymers1564
Water18,5011027
1
A: Retron-type reverse transcriptase
C: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9144
Polymers69,8362
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-4 kcal/mol
Surface area24630 Å2
MethodPISA
2
B: Retron-type reverse transcriptase
D: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9144
Polymers69,8362
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-6 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.290, 79.160, 86.020
Angle α, β, γ (deg.)109.00, 90.56, 105.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Retron-type reverse transcriptase


Mass: 34918.109 Da / Num. of mol.: 4 / Fragment: UNP residues 1-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia intestinalis XB6B4 (bacteria)
Gene: RO1_37670 / Production host: Escherichia coli (E. coli) / References: UniProt: D4L313
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1027 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Bis-Tris propane pH 8.5, 200 mM NaOAc-3H2O, 20% PEG 3350

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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: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→46.47 Å / Num. obs: 152938 / % possible obs: 96.1 % / Redundancy: 3.9 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2254: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHJ

5hhj


Resolution: 1.6→46.47 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 7642 5 %
Rwork0.1906 --
obs0.1924 152861 96.17 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9179 0 4 1027 10210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069644
X-RAY DIFFRACTIONf_angle_d0.78413046
X-RAY DIFFRACTIONf_dihedral_angle_d12.856095
X-RAY DIFFRACTIONf_chiral_restr0.0511438
X-RAY DIFFRACTIONf_plane_restr0.0051711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6004-1.61850.46292240.41924255X-RAY DIFFRACTION84
1.6185-1.63760.37622500.33564740X-RAY DIFFRACTION95
1.6376-1.65760.36732510.33774790X-RAY DIFFRACTION95
1.6576-1.67850.36572550.31464847X-RAY DIFFRACTION95
1.6785-1.70060.34022470.30044707X-RAY DIFFRACTION95
1.7006-1.72390.36372570.29094876X-RAY DIFFRACTION95
1.7239-1.74860.33572540.27574823X-RAY DIFFRACTION96
1.7486-1.77470.3092500.24744736X-RAY DIFFRACTION96
1.7747-1.80240.26662560.22534887X-RAY DIFFRACTION96
1.8024-1.83190.26932530.21894800X-RAY DIFFRACTION96
1.8319-1.86350.30552550.21684871X-RAY DIFFRACTION96
1.8635-1.89740.25872540.21944821X-RAY DIFFRACTION96
1.8974-1.93390.26912570.22624882X-RAY DIFFRACTION96
1.9339-1.97340.26782540.21874821X-RAY DIFFRACTION97
1.9734-2.01630.27022570.20274890X-RAY DIFFRACTION97
2.0163-2.06320.24092540.19064831X-RAY DIFFRACTION97
2.0632-2.11480.2622580.19564886X-RAY DIFFRACTION97
2.1148-2.1720.22332580.18694906X-RAY DIFFRACTION97
2.172-2.23590.22952570.1844882X-RAY DIFFRACTION97
2.2359-2.30810.26582580.18354904X-RAY DIFFRACTION97
2.3081-2.39050.2422600.19024935X-RAY DIFFRACTION98
2.3905-2.48620.22712580.1824900X-RAY DIFFRACTION98
2.4862-2.59940.22222580.18214914X-RAY DIFFRACTION98
2.5994-2.73640.20452610.18064949X-RAY DIFFRACTION98
2.7364-2.90780.19722580.17564910X-RAY DIFFRACTION98
2.9078-3.13230.21772620.18084964X-RAY DIFFRACTION98
3.1323-3.44740.20322580.17134917X-RAY DIFFRACTION98
3.4474-3.94610.16272610.15194949X-RAY DIFFRACTION98
3.9461-4.97070.17192620.1514977X-RAY DIFFRACTION99
4.9707-46.48960.2082450.18774649X-RAY DIFFRACTION93

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