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

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Basic information

Entry
Database: PDB / ID: 6doo
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 100 mM K+ for 120 s at 21 C (dataset 2)
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • 5'-R(P*CP*G)-3' portion of cleaved RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • Ribonuclease H
KeywordsHYDROLASE/DNA/RNA / protein-RNA-DNA complex / double helix / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / monovalent cations / divalent cations / HYDROLASE-DNA-RNA 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 / : / TRIETHYLENE GLYCOL / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 15, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.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.ptnr1_symmetry / _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.ptnr2_symmetry

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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 cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
b: 5'-R(P*CP*G)-3' portion of cleaved 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)20,71720
Polymers19,3714
Non-polymers1,34616
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-33 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.478, 37.716, 62.358
Angle α, β, γ (deg.)90.000, 96.210, 90.000
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 cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'


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


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

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 15716.729 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 61-196)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.) synthetic construct (others)

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Non-polymers , 7 types, 200 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.45 Å3/Da / Density % sol: 49.86 % / Mosaicity: 0 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 20% glycerol, 200 mM potassium iodide, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2016
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→19.27 Å / Num. obs: 34017 / % possible obs: 99.1 % / Redundancy: 1 % / Biso Wilson estimate: 19.71 Å2 / Net I/σ(I): 6.8 / Num. measured all: 34017
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.44-1.4611455187.6
7.89-19.271209190.9

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZBL

1zbl


Resolution: 1.44→19.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.66
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1702 1680 4.94 %
Rwork0.1449 --
obs0.1461 34010 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.56 Å2 / Biso mean: 30.8905 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 1.44→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 53 184 1591
Biso mean--56.59 44.68 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091519
X-RAY DIFFRACTIONf_angle_d1.2052083
X-RAY DIFFRACTIONf_chiral_restr0.079231
X-RAY DIFFRACTIONf_plane_restr0.007213
X-RAY DIFFRACTIONf_dihedral_angle_d23.404606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4404-1.48280.33111240.31812491261592
1.4828-1.53070.26771440.27622661280599
1.5307-1.58530.28071370.224227122849100
1.5853-1.64880.23241570.201226522809100
1.6488-1.72380.20851350.176927052840100
1.7238-1.81460.19351370.162826992836100
1.8146-1.92820.17111420.150927192861100
1.9282-2.07690.17941510.13726952846100
2.0769-2.28560.15371370.129727222859100
2.2856-2.61560.16321410.135627392880100
2.6156-3.29270.16061210.135427552876100
3.2927-19.27170.14391540.12422780293499
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)
13.94060.77112.39363.8463-0.39723.31390.07360.70860.014-0.3212-0.2634-0.84390.26191.65520.28080.23970.11460.07060.56420.0320.259940.5148-4.521718.9012
23.0157-1.15064.27421.8654-1.03896.43520.3330.205-0.3645-0.1857-0.15490.10790.3727-0.0758-0.19730.2125-0.0009-0.01490.2049-0.00190.136219.836-6.196816.8198
34.01022.0297-5.65737.9315-0.77559.0083-0.1756-0.657-1.03380.0753-0.0024-0.55590.85460.5480.13770.26040.0663-0.02320.21470.05660.226828.12-11.587824.1019
43.5021-0.11551.97020.9760.1583.56670.083-0.2442-0.1111-0.015-0.07690.03170.0537-0.23090.00280.17080.01550.01310.18410.00440.109521.685-1.22323.4554
56.1236-3.17790.6335.28071.79951.70630.20720.31840.428-0.487-0.166-0.3371-0.8992-0.0655-0.06030.32110.00580.02030.1780.0460.147123.90459.370716.6701
67.81591.25722.43051.89870.3445.39890.2223-0.08360.5384-0.0676-0.4390.4961-0.6975-1.1920.14390.33510.2359-0.02640.4623-0.08580.1878.59597.533716.1655
77.49542.08185.13942.3823.23368.28260.1855-0.2481-0.01450.0194-0.30670.1285-0.1887-0.77310.15150.19320.06760.00920.2717-0.03090.119912.44175.738524.9543
84.6871-5.3182-6.15337.13366.28628.54570.1012-0.49180.3678-0.11590.18-0.2807-0.34370.2704-0.22410.2283-0.0023-0.01360.252-0.01220.136226.50158.423930.4162
90.3554-0.4629-0.51855.27673.89062.99440.20290.3996-0.0393-0.5721-0.2186-0.4244-0.06970.2981-0.06850.27570.08120.06790.39160.03470.160134.6493-0.823112.4358
107.32620.9463-6.95474.00650.27077.673-0.20040.7103-0.5075-0.78980.03180.22770.6491-0.14030.17590.43250.0607-0.03490.2788-0.05890.175125.2522-9.691711.6956
113.96390.44222.55255.04840.11162.14820.0510.3464-0.143-0.6308-0.2292-0.24110.11690.20330.18940.33570.07670.02450.29610.02850.131123.7640.44035.4349
122.301-1.1419-1.94360.63370.37537.2941-0.01120.2636-0.1295-0.7934-0.31120.13-0.2625-0.29550.31590.45420.0971-0.03560.2936-0.01620.153916.40523.44833.2813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )A61 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 87 )A67 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 96 )A88 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 133 )A97 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 142 )A134 - 142
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )A143 - 155
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 169 )A156 - 169
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 177 )A170 - 177
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 186 )A178 - 186
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 196 )A187 - 196
11X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4)) or (chain 'b' and (resid 5 through 6))B1 - 4
12X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4)) or (chain 'b' and (resid 5 through 6))b5 - 6
13X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )C1 - 6

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