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

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Basic information

Entry
Database: PDB / ID: 5hhj
TitleReverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P21 space group
ComponentsRetron-type reverse transcriptase
KeywordsRNA BINDING PROTEIN / Group II intron
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
GLYCINE / : / PHOSPHATE ION / SUCCINIC ACID / Retron-type reverse transcriptase
Similarity search - Component
Biological speciesRoseburia intestinalis XB6B4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 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
DepositionJan 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,56611
Polymers69,8362
Non-polymers7309
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-25 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.080, 88.060, 79.760
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Retron-type reverse transcriptase


Mass: 34918.109 Da / Num. of mol.: 2 / 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

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Non-polymers , 6 types, 796 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100 mM SPG pH 9.0, 23% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.2→44.03 Å / Num. obs: 178024 / % possible obs: 99 % / Redundancy: 6.4 % / Net I/σ(I): 16.04

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Processing

Software
NameVersionClassification
PHENIX(dev_2254: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5HHK

5hhk


Resolution: 1.2→44.03 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1475 8900 5 %
Rwork0.1229 --
obs0.1242 178006 98.85 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 43 787 5527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015142
X-RAY DIFFRACTIONf_angle_d1.1226990
X-RAY DIFFRACTIONf_dihedral_angle_d16.7762111
X-RAY DIFFRACTIONf_chiral_restr0.087767
X-RAY DIFFRACTIONf_plane_restr0.008922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.22032730.23785197X-RAY DIFFRACTION93
1.2136-1.22790.22252910.19745521X-RAY DIFFRACTION97
1.2279-1.24290.18332950.15365608X-RAY DIFFRACTION98
1.2429-1.25860.19352940.15015582X-RAY DIFFRACTION98
1.2586-1.27520.16792960.14115626X-RAY DIFFRACTION98
1.2752-1.29270.17342950.13225533X-RAY DIFFRACTION99
1.2927-1.31110.1642940.12525663X-RAY DIFFRACTION99
1.3111-1.33070.1452960.11985600X-RAY DIFFRACTION99
1.3307-1.35150.13922990.11495700X-RAY DIFFRACTION99
1.3515-1.37370.14832960.11415644X-RAY DIFFRACTION99
1.3737-1.39730.1543020.10895716X-RAY DIFFRACTION99
1.3973-1.42280.14492910.10765567X-RAY DIFFRACTION100
1.4228-1.45010.13423030.10325713X-RAY DIFFRACTION100
1.4501-1.47970.15612960.10295619X-RAY DIFFRACTION100
1.4797-1.51190.1382990.09835693X-RAY DIFFRACTION100
1.5119-1.54710.1182970.09255665X-RAY DIFFRACTION99
1.5471-1.58580.12772960.09455602X-RAY DIFFRACTION99
1.5858-1.62860.12852990.09755705X-RAY DIFFRACTION100
1.6286-1.67660.1422990.15663X-RAY DIFFRACTION100
1.6766-1.73070.13782990.10565682X-RAY DIFFRACTION100
1.7307-1.79250.13572980.10475657X-RAY DIFFRACTION100
1.7925-1.86430.1442980.11115683X-RAY DIFFRACTION100
1.8643-1.94920.13952980.11235674X-RAY DIFFRACTION99
1.9492-2.05190.12092970.11385618X-RAY DIFFRACTION99
2.0519-2.18050.13273000.11195704X-RAY DIFFRACTION100
2.1805-2.34880.13213010.11265721X-RAY DIFFRACTION100
2.3488-2.58520.13383000.1215700X-RAY DIFFRACTION100
2.5852-2.95920.15542940.13365593X-RAY DIFFRACTION98
2.9592-3.7280.15253020.13085728X-RAY DIFFRACTION99
3.728-44.05960.16823020.14545729X-RAY DIFFRACTION98

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