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

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Basic information

Entry
Database: PDB / ID: 6dpd
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 16 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Components
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • RNA (5'-R(*AP*CP*AP*U)-3')
  • RNA (5'-R(P*CP*G)-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


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 / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / 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 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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.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: RNA (5'-R(*AP*CP*AP*U)-3')
b: RNA (5'-R(P*CP*G)-3')
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,04924
Polymers19,3714
Non-polymers1,67820
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-41 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.324, 37.988, 61.323
Angle α, β, γ (deg.)90.00, 96.32, 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 RNA (5'-R(*AP*CP*AP*U)-3')


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


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / 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.) synthetic (others)

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Non-polymers , 7 types, 206 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsNote that chain B was split into 2 chains (B and b) at the position 4-5, where the cleavage occurs

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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: 2.42 Å3/Da / Density % sol: 49.27 % / 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: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→19.84 Å / Num. obs: 32500 / % possible obs: 99 % / Redundancy: 1 % / Biso Wilson estimate: 19.53 Å2 / Net I/σ(I): 6.7 / Num. measured all: 32500
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 1 % / Num. unique obs: 1401 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZBL

1zbl


Resolution: 1.46→19.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.93
Details: STRUCTURES REFINED IN PHENIX AND NUCLEIC ACID AND PROTEIN RESIDUES BUILT IN COOT
RfactorNum. reflection% reflection
Rfree0.173 1642 5.05 %
Rwork0.151 --
obs0.152 32488 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.41 Å2
Refinement stepCycle: LAST / Resolution: 1.46→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 56 186 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071467
X-RAY DIFFRACTIONf_angle_d0.962020
X-RAY DIFFRACTIONf_dihedral_angle_d22.917573
X-RAY DIFFRACTIONf_chiral_restr0.068219
X-RAY DIFFRACTIONf_plane_restr0.006211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4556-1.49840.30581230.29352381X-RAY DIFFRACTION92
1.4984-1.54680.28261360.25292557X-RAY DIFFRACTION99
1.5468-1.6020.26741270.2272582X-RAY DIFFRACTION99
1.602-1.66610.24151470.20212562X-RAY DIFFRACTION99
1.6661-1.74190.18321300.18462535X-RAY DIFFRACTION99
1.7419-1.83370.22641340.17722583X-RAY DIFFRACTION99
1.8337-1.94850.20861540.17172593X-RAY DIFFRACTION100
1.9485-2.09880.16991400.15342551X-RAY DIFFRACTION99
2.0988-2.30970.17961360.15052595X-RAY DIFFRACTION99
2.3097-2.64330.20161440.15152604X-RAY DIFFRACTION99
2.6433-3.32770.17161430.14352600X-RAY DIFFRACTION100
3.3277-19.84650.11681280.11842703X-RAY DIFFRACTION100
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)
13.1907-0.50951.65161.9977-0.48454.35940.17010.2361-0.1909-0.0846-0.1298-0.14060.23480.3703-0.050.15980.03120.03450.1444-0.00450.110425.07-5.74116.692
27.338-2.6658-7.07859.74781.46428.7435-0.0715-0.2803-1.2940.2149-0.1527-0.30720.69810.53370.18280.27910.0684-0.01240.2260.05080.268828.028-11.66323.511
38.3239-2.23872.59154.7374-5.70066.90480.0947-0.3251-0.4017-0.05670.31430.52190.1834-0.8446-0.36020.2316-0.01-0.00060.287-0.0410.192410.365-4.98518.253
44.6718-1.33752.50761.81420.28385.08630.084-0.03150.0417-0.0355-0.0601-0.0671-0.1214-0.0101-0.04710.1561-0.00650.03720.11540.0080.122124.6311.89522.419
52.8585-0.55653.35222.69020.31386.48380.03870.00230.4573-0.1957-0.26460.544-0.6291-0.84810.28830.33040.17280.01820.3607-0.07660.21189.6188.16516.101
68.42741.02535.50963.73281.45236.38380.1232-0.17190.1094-0.0135-0.26240.1855-0.1212-0.59820.15950.21820.05290.04830.2435-0.02860.13412.4325.79824.51
75.5667-4.8527-1.22756.11083.85164.38650.0907-0.46420.5802-0.04420.2444-0.4713-0.32950.4098-0.33510.2536-0.01280.02970.2096-0.00390.198326.4758.36229.946
80.56570.10871.58318.54386.11498.33260.16070.48310.0875-0.55050.0245-0.5372-0.11150.5746-0.19660.24010.04090.07770.34870.02280.17334.378-0.8411.905
97.71373.4614-1.52556.51962.13635.24480.03480.5675-0.4055-0.28310.05790.08720.3960.1874-0.05470.32530.0881-0.00290.1987-0.04210.163725.126-9.68511.106
102.1688-1.63542.42466.5897-0.51383.05760.11710.30820.1486-0.6255-0.3811-0.44790.03020.30680.28510.33130.08240.07110.29910.02620.151523.7961.2174.296
111.7882-1.5401-2.71363.22241.71544.32030.04440.1934-0.0782-0.8099-0.37370.1512-0.6791-0.25730.31420.43340.0818-0.01540.24870.00950.146616.4013.6062.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:87 )A61 - 87
2X-RAY DIFFRACTION2( CHAIN A AND RESID 88:96 )A88 - 96
3X-RAY DIFFRACTION3( CHAIN A AND RESID 97:104 )A97 - 104
4X-RAY DIFFRACTION4( CHAIN A AND RESID 105:141 )A105 - 141
5X-RAY DIFFRACTION5( CHAIN A AND RESID 142:155 )A142 - 155
6X-RAY DIFFRACTION6( CHAIN A AND RESID 156:169 )A156 - 169
7X-RAY DIFFRACTION7( CHAIN A AND RESID 170:177 )A170 - 177
8X-RAY DIFFRACTION8( CHAIN A AND RESID 178:186 )A178 - 186
9X-RAY DIFFRACTION9( CHAIN A AND RESID 187:196 )A187 - 196
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
11X-RAY DIFFRACTION10( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
12X-RAY DIFFRACTION11( CHAIN C AND RESID 1:6 )C1 - 6

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