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- PDB-6ar1: Structure of a Thermostable Group II Intron Reverse Transcriptase... -

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Basic information

Entry
Database: PDB / ID: 6ar1
TitleStructure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (RT/Duplex (Nat))
Components
  • DNA
  • GsI-IIC RT
  • RNA
KeywordsRNA binding protein/RNA/DNA / Polymerase / RNA binding protein-RNA-DNA complex
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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10) / Trt
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsStamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 37949 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 37951 United States
Robert A. Welch FoundationF-1607 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications.
Authors: Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GsI-IIC RT
B: DNA
C: RNA
D: GsI-IIC RT
E: DNA
F: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,35612
Polymers115,1336
Non-polymers1,2236
Water0
1
A: GsI-IIC RT
B: DNA
C: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1786
Polymers57,5673
Non-polymers6123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-35 kcal/mol
Surface area23060 Å2
MethodPISA
2
D: GsI-IIC RT
E: DNA
F: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1786
Polymers57,5673
Non-polymers6123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.151, 95.052, 71.567
Angle α, β, γ (deg.)90.000, 113.550, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12C
22F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA2 - 4182 - 418
21ALAALAARGARGDD2 - 4182 - 418
12UUGGCC1 - 141 - 14
22UUGGFF1 - 141 - 14

NCS ensembles :
ID
1
2

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Components

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Protein / DNA chain / RNA chain , 3 types, 6 molecules ADBECF

#1: Protein GsI-IIC RT


Mass: 49805.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trt / Production host: Escherichia coli (E. coli) / References: UniProt: E2GM63
#2: DNA chain DNA /


Mass: 3303.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA /


Mass: 4457.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.498
11H+4/2L, -K, -L20.502
ReflectionResolution: 3.01→47.53 Å / Num. obs: 21941 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.044 / Rrim(I) all: 0.121 / Net I/σ(I): 16.2 / Num. measured all: 166560 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.01-3.197.60.85234970.8860.330.91499.1
9.03-47.537.30.02383910.0090.02599.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSMay 1, 2016data reduction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AR3

6ar3


Resolution: 3.01→47.53 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.927 / SU B: 45.567 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED Twin refinement in Refmac5 with twin fraction = 0.5, twin operator = h+2*l, -k, -l.
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1092 5 %RANDOM
Rwork0.2164 ---
obs0.2184 20847 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.72 Å2 / Biso mean: 87.267 Å2 / Biso min: 49.35 Å2
Baniso -1Baniso -2Baniso -3
1--48.14 Å2-0 Å2-29.17 Å2
2--66.15 Å20 Å2
3----18.01 Å2
Refinement stepCycle: final / Resolution: 3.01→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 1005 72 0 7873
Biso mean--81.72 --
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0188132
X-RAY DIFFRACTIONr_angle_refined_deg1.171.85211182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20221.791335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5551598
X-RAY DIFFRACTIONr_chiral_restr0.0810.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215827
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A268280.08
12D268280.08
21C25040.01
22F25040.01
LS refinement shellResolution: 3.01→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 75 -
Rwork0.318 1517 -
all-1592 -
obs--98.33 %
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)
14.1449-0.60631.31381.4272-0.02133.24280.1942-0.0861-0.1461-0.2087-0.08180.57190.4083-0.5761-0.11250.374-0.1504-0.10150.2560.01840.25244.1087-42.320231.1723
22.2145-0.4661.02651.70440.11072.4883-0.2683-0.20570.7654-0.17960.10630.5582-0.4303-0.88850.16210.3718-0.0216-0.16830.43870.10.65067.002-21.434623.5013
34.8164-0.63192.17350.76940.43262.8377-0.0803-0.4251-0.15490.13910.1896-0.10580.01670.2975-0.10930.3642-0.1163-0.00540.24070.08290.283441.6028-25.010233.9807
43.20080.75581.33758.2072.14542.98820.19880.3952-1.0198-0.1676-0.16470.45310.77760.0236-0.03410.38080.00620.03890.2249-0.05820.483523.2298-38.109324.4221
54.8548-0.06351.97833.823-1.94853.47920.2353-0.0162-0.7031-0.1029-0.0905-0.49290.67020.3665-0.14480.3417-0.0272-0.04440.1664-0.00620.269222.9314-39.339125.0978
63.7996-0.7635-0.22621.53191.15272.9629-0.0123-0.5855-0.1210.28640.1258-0.45870.17430.4936-0.11350.2328-0.0807-0.03870.2717-0.01960.317266.0505-17.882914.7309
74.75370.4580.85423.75841.211.36830.1799-0.2046-2.11230.8291-0.1374-0.26080.81950.4335-0.04240.70550.21170.11520.40360.22191.164763.5415-38.01856.4202
86.9884-0.14471.2410.0664-0.20681.0840.1107-0.15330.5109-0.05180.04850.1133-0.085-0.429-0.15930.37650.0287-0.04090.357-0.1040.40231.5799-22.9338-8.8563
96.7535-1.3453-0.72028.0804-1.76550.74140.9889-0.14911.31160.9768-1.0925-0.0581-0.63530.22990.10360.6242-0.1281-0.130.2461-0.12620.655953.9169-12.70630.3452
104.901-2.72520.86473.49580.79986.22380.07560.38020.8555-0.8201-0.09560.2204-0.7876-0.67360.020.4796-0.1713-0.16190.36670.12210.486354.9476-11.19480.1362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION2A77 - 249
3X-RAY DIFFRACTION2A501
4X-RAY DIFFRACTION2A503
5X-RAY DIFFRACTION3A250 - 418
6X-RAY DIFFRACTION4B1 - 11
7X-RAY DIFFRACTION5C1 - 14
8X-RAY DIFFRACTION6D2 - 188
9X-RAY DIFFRACTION7D189 - 282
10X-RAY DIFFRACTION7D501
11X-RAY DIFFRACTION7D503
12X-RAY DIFFRACTION8D283 - 418
13X-RAY DIFFRACTION9E2 - 11
14X-RAY DIFFRACTION10F1 - 14

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