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

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Basic information

Entry
Database: PDB / ID: 5irg
TitleReverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P212121 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 / RNA-directed DNA polymerase activity / defense response to virus / DNA damage response / 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
: / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesRoseburia intestinalis XB6B4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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.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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)142,4558
Polymers142,2994
Non-polymers1564
Water5,477304
1
A: Retron-type reverse transcriptase
D: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2274
Polymers71,1492
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-4 kcal/mol
Surface area24460 Å2
MethodPISA
2
B: Retron-type reverse transcriptase
C: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2274
Polymers71,1492
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-4 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.810, 145.350, 200.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Retron-type reverse transcriptase


Mass: 35574.637 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.: 304 / 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: 44.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM MMT pH 8.0, 25% PEG 1500

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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: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→49.135 Å / Num. obs: 57600 / % possible obs: 99.8 % / Redundancy: 7.1 % / Net I/σ(I): 16.9
Reflection shellHighest resolution: 2.3 Å

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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
Resolution: 2.3→49.135 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 2841 4.98 %
Rwork0.1906 --
obs0.1926 54596 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9190 0 4 304 9498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029359
X-RAY DIFFRACTIONf_angle_d0.4312597
X-RAY DIFFRACTIONf_dihedral_angle_d13.2025779
X-RAY DIFFRACTIONf_chiral_restr0.0411384
X-RAY DIFFRACTIONf_plane_restr0.0031647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32620.32221780.28863413X-RAY DIFFRACTION100
2.3262-2.35350.28211880.27183417X-RAY DIFFRACTION100
2.3535-2.38220.32451780.27073408X-RAY DIFFRACTION100
2.3822-2.41240.32631680.26133350X-RAY DIFFRACTION100
2.4124-2.44410.31411830.26323391X-RAY DIFFRACTION100
2.4441-2.47760.30851820.25613347X-RAY DIFFRACTION100
2.4776-2.5130.2741790.24543483X-RAY DIFFRACTION100
2.513-2.55050.30911760.24533347X-RAY DIFFRACTION100
2.5505-2.59040.30331790.24693390X-RAY DIFFRACTION100
2.5904-2.63280.28751780.23483381X-RAY DIFFRACTION100
2.6328-2.67820.29031810.23133458X-RAY DIFFRACTION100
2.6782-2.72690.25541700.22323345X-RAY DIFFRACTION100
2.7269-2.77940.23791850.21333358X-RAY DIFFRACTION100
2.7794-2.83610.22771760.20493441X-RAY DIFFRACTION100
2.8361-2.89770.26181740.20963350X-RAY DIFFRACTION100
2.8977-2.96510.29961690.22343393X-RAY DIFFRACTION100
2.9651-3.03930.29371780.21443439X-RAY DIFFRACTION100
3.0393-3.12150.25441750.20333355X-RAY DIFFRACTION100
3.1215-3.21330.21891800.19083402X-RAY DIFFRACTION100
3.2133-3.3170.27951780.19223407X-RAY DIFFRACTION100
3.317-3.43550.20491810.1863341X-RAY DIFFRACTION100
3.4355-3.5730.21591880.18243447X-RAY DIFFRACTION100
3.573-3.73560.21791720.16893340X-RAY DIFFRACTION100
3.7356-3.93240.17571780.15683424X-RAY DIFFRACTION100
3.9324-4.17870.19461780.1523363X-RAY DIFFRACTION100
4.1787-4.50110.1981720.15243355X-RAY DIFFRACTION100
4.5011-4.95370.19871700.15053411X-RAY DIFFRACTION100
4.9537-5.66960.20171780.1683389X-RAY DIFFRACTION100
5.6696-7.13960.22711750.18733424X-RAY DIFFRACTION100
7.1396-49.14670.17581790.16953357X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5571-0.1860.22951.078-0.18760.11570.20930.58590.0121-0.4803-0.37090.0951-0.3735-0.5575-0.24070.59220.3471-0.08730.6663-0.07140.321525.327962.178482.4036
20.9897-0.18570.26921.0429-0.34160.25670.04140.4164-0.0272-0.4185-0.1336-0.34110.0206-0.0077-0.2970.31280.0868-0.06230.507-0.11530.349835.681851.339282.9168
30.90110.29970.09320.86540.17130.05160.37340.0983-0.1410.1285-0.45890.1282-0.2307-0.443-0.08540.10620.2831-0.03680.2449-0.06240.237723.662258.7406101.1172
40.11010.20920.02220.71090.23240.13220.01090.2536-0.33950.1468-0.20490.34090.1593-0.6299-1.0580.12150.0461-0.1650.5396-0.22840.31220.422145.63397.9951
50.06730.0551-0.04810.0362-0.03040.05250.1798-0.0755-0.2316-0.0024-0.2572-0.04740.0818-0.2901-00.29330.0592-0.05420.3715-0.06030.406634.558751.845298.2934
60.18280.35890.18011.54040.26970.24570.16260.0807-0.21160.1694-0.17040.25490.1161-0.25120.08960.15190.0387-0.04780.3882-0.0910.359318.958850.5365108.6396
70.2723-0.1794-0.10810.56550.47610.4152-0.16170.048-0.69030.2489-0.29480.34230.2689-0.4312-0.24560.3614-0.12510.03720.318-0.06490.528216.588640.4506116.4526
80.55050.41070.06610.6874-0.15550.12920.05270.075-0.3530.4254-0.0235-0.21840.09190.1918-0.03670.26670.0068-0.04730.202-0.01170.308830.903351.2755119.609
90.0357-0.0280.01820.0165-0.01750.08270.12660.2742-0.5808-0.55080.10250.17990.5549-0.08580.00140.552-0.0111-0.02870.4592-0.01840.512511.151691.0838147.7942
100.00450.0231-0.01470.08870.03430.13010.0026-0.3665-0.54790.0903-0.0529-0.37910.84880.4924-0.00010.58660.0894-0.0340.58270.12160.671819.58187.0661155.9788
110.2678-0.1657-0.15180.34370.13270.2301-0.0327-0.1230.0170.0595-0.0194-0.14980.01480.3456-00.2656-0.0131-0.01870.44410.03760.364717.4108100.4086157.3126
120.41870.30360.08610.37130.22350.16280.02770.1790.1620.02820.16110.2229-0.23230.1700.3529-0.02140.02360.3870.00540.32968.8733120.1538149.7132
130.0606-0.1523-0.07140.32510.17120.3250.0392-0.04180.25140.22890.21830.2568-0.23580.14650.00010.2970.01750.03130.48790.03550.37019.8781104.3706158.5685
140.06360.01640.01350.07480.03040.00960.0693-0.15340.12060.38890.06540.4306-0.2026-0.036-00.3356-0.01010.07220.4160.02590.37664.0061119.3771153.4551
150.3597-0.30520.55520.3125-0.51610.91590.2996-0.36660.3620.18080.20330.2388-0.2959-0.35310.07230.59950.03210.17610.4507-0.05390.4631.7691129.863161.5401
160.02920.01420.04120.0490.07760.1244-0.1243-0.04380.09590.22510.2012-0.102-0.2931-0.0088-00.5009-0.05250.05740.403-0.09230.360212.4361127.1081158.5451
170.0290.03360.00760.04450.02570.03540.3535-0.26740.3217-0.30690.0657-0.1968-0.36430.34070.00010.5664-0.07860.050.4574-0.01360.537419.0035132.9073141.4475
180.4660.2686-0.430.3064-0.25970.40020.20260.27720.35150.02110.22540.6517-0.4596-0.1590.08570.61650.04070.0260.4270.19520.62811.9124134.8968121.0484
190.0617-0.0642-0.12130.08660.12950.2130.23770.14680.33770.08610.0582-0.0729-0.23240.10970.01870.6526-0.1460.04380.3450.05430.381316.8874136.8883118.8667
200.3150.1058-0.10030.2581-0.30860.3586-0.02350.03470.0392-0.24930.0497-0.06420.01270.151100.5027-0.03930.04350.44140.03370.464318.3015116.227126.7608
210.53190.1467-0.30970.257-0.31540.3680.03360.06010.0627-0.3779-0.0631-0.10930.15140.255700.718-0.05760.01220.36060.05070.404916.8835121.3743118.2147
220.33380.19280.10250.43190.1880.1273-0.0010.0274-0.1583-0.36350.065-0.4878-0.10450.75810.00340.4016-0.03960.13950.5616-0.00620.462531.8684110.4111129.7385
231.0922-0.16180.66110.4879-0.02380.9626-0.0117-0.45760.09170.5398-0.03640.2326-0.1039-0.5268-0.0090.49880.05060.02480.3428-0.03190.32422.310779.6072131.3747
240.8975-0.2619-0.16081.22740.04211.03470.1301-0.01470.08280.0365-0.1084-0.1363-0.41710.136600.3463-0.04190.00140.23440.02540.293738.080678.8999110.6257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 188 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 246 )
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 303 )
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 38 )
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 69 )
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 115 )
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 210 )
14X-RAY DIFFRACTION14chain 'B' and (resid 211 through 246 )
15X-RAY DIFFRACTION15chain 'B' and (resid 247 through 263 )
16X-RAY DIFFRACTION16chain 'B' and (resid 264 through 286 )
17X-RAY DIFFRACTION17chain 'B' and (resid 287 through 304 )
18X-RAY DIFFRACTION18chain 'C' and (resid 15 through 68 )
19X-RAY DIFFRACTION19chain 'C' and (resid 69 through 96 )
20X-RAY DIFFRACTION20chain 'C' and (resid 97 through 162 )
21X-RAY DIFFRACTION21chain 'C' and (resid 163 through 228 )
22X-RAY DIFFRACTION22chain 'C' and (resid 229 through 304 )
23X-RAY DIFFRACTION23chain 'D' and (resid 15 through 96 )
24X-RAY DIFFRACTION24chain 'D' and (resid 97 through 304 )

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