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- PDB-6doi: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6doi
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid (1.54 Angstrom wavelength): Soak in 0.5 mM EGTA and 200 mM K+ at 21 C
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
  • 5'-R(P*CP*G)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • Ribonuclease H
KeywordsHYDROLASE/RNA/DNA / protein-RNA-DNA complex / double helix / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / monovalent cations / divalent cations / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 ...Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / Resolution: 1.948 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Cation trafficking propels RNA hydrolysis.
Authors: Samara, N.L. / Yang, W.
History
DepositionJun 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
b: 5'-R(P*CP*G)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,18518
Polymers19,0284
Non-polymers1,15814
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-30 kcal/mol
Surface area7870 Å2
Unit cell
Length a, b, c (Å)81.456, 38.020, 62.071
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 2 types, 2 molecules Bb

#2: RNA chain 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')


Mass: 1224.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: RNA chain 5'-R(P*CP*G)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 15373.304 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KEI9, ribonuclease H
#4: DNA chain DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')


Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 6 types, 178 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.5 Å3/Da / Density % sol: 50.9 % / Mosaicity: 0 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 20% glycerol, 200 mM KI, and 25 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→22.01 Å / Num. obs: 12950 / % possible obs: 92.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.6 / % possible all: 78.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: PDBID 1ZBL

1zbl


Resolution: 1.948→22.01 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 608 4.7 %
Rwork0.147 --
obs0.1494 12947 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 243 40 164 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091444
X-RAY DIFFRACTIONf_angle_d1.0372003
X-RAY DIFFRACTIONf_dihedral_angle_d19.92825
X-RAY DIFFRACTIONf_chiral_restr0.057220
X-RAY DIFFRACTIONf_plane_restr0.007209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9479-2.14370.23051400.17472889X-RAY DIFFRACTION87
2.1437-2.45360.21921440.15723088X-RAY DIFFRACTION94
2.4536-3.08990.20841600.16023146X-RAY DIFFRACTION94
3.0899-22.0110.17371640.13163216X-RAY DIFFRACTION94
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)
17.26334.5551-0.71633.9281-1.65943.83040.21021.13310.1451-0.2445-0.154-0.62850.24910.93430.19790.21110.13630.02960.4698-0.01070.355240.7886-3.936918.7799
23.1505-3.00641.51024.0298-0.06012.3270.4263-0.2146-0.3371-0.1838-0.269-0.01940.3694-0.2684-0.35880.2080.0010.0230.21720.03470.138223.2789-5.835917.331
37.5737-3.35887.39862.0262-3.28137.43910.39890.595-0.2647-0.1714-0.42710.02320.36510.3942-0.13460.23170.0043-0.00850.1995-0.03960.243317.922-6.298616.5342
45.38020.1549-5.28263.6476-0.13775.2031-0.0478-0.261-1.2870.066-0.0437-0.47560.65310.39590.17190.25460.026-0.00150.17230.01430.347827.5306-11.463223.7589
53.6286-0.8152.2270.95130.15643.94570.0114-0.0746-0.0129-0.0522-0.06010.0296-0.1111-0.21930.04950.133-0.00460.02780.07390.00260.155622.42880.870921.9882
63.69632.95762.9814.24441.06464.57040.46480.05490.3171-0.2259-0.44310.2665-0.689-0.66610.07720.34670.2482-0.00290.3696-0.11380.25269.637.897216.5349
77.43561.61185.93764.55463.23817.15430.0662-0.45990.125-0.1378-0.38870.267-0.1939-0.75810.33030.19880.07320.03190.2618-0.04060.208412.42365.773424.9175
85.9096-6.9429-4.76618.28895.81034.31020.1049-0.20190.528-0.31460.0361-0.1802-0.69290.0476-0.04890.2061-0.01160.00070.1699-0.00210.201226.43778.565330.3022
94.3262-1.39970.05693.78234.42545.87370.4540.9888-0.1734-0.4932-0.3996-0.42860.06810.3331-0.2390.26810.06930.06620.32520.02020.203634.7224-0.451112.3826
101.408-0.1044-1.49336.6756-5.93458.9098-1.01630.8225-1.0017-0.53870.29490.26570.8007-2.02730.89470.58590.26590.14430.7623-0.25240.282427.6764-9.216613.2168
114.5452-1.30973.73531.9336-2.02625.80080.01340.5008-0.0852-0.6766-0.2522-0.27640.09740.27260.23170.26750.06790.04410.2181-0.01230.179923.82791.45744.5056
123.9644-1.4631-0.82542.68773.90189.37250.05640.3556-0.1273-1.0327-0.38140.0826-0.546-0.22870.28380.43710.0821-0.02160.2102-0.00770.174916.41513.69593.2538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 169 )
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 186 )
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 193 )
11X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4 )) or (chain 'b' and (resid 5 through 6))
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )

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