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

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Basic information

Entry
Database: PDB / ID: 6dpb
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 8 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') portion of cleaved RNA
  • RNA (5'-R(P*CP*G)-3') portion of cleaved RNA
  • 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 / : / : / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.324 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 / 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.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_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.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.ptnr2_symmetry / _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: RNA (5'-R(*AP*CP*AP*U)-3') portion of cleaved RNA
b: RNA (5'-R(P*CP*G)-3') portion of cleaved RNA
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,77022
Polymers19,3714
Non-polymers1,39918
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-37 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.546, 37.318, 62.154
Angle α, β, γ (deg.)90.000, 96.850, 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 RNA (5'-R(*AP*CP*AP*U)-3') portion of cleaved RNA


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') portion of cleaved RNA


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 , 6 types, 230 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe RNA chain B was split into 2 chains (B and b)
Sequence detailsThe RNA 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: 49.13 % / 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: 22-BM / 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: 1.32→33.89 Å / Num. obs: 41029 / % possible obs: 94.8 % / Redundancy: 1 % / Biso Wilson estimate: 18.36 Å2 / Net I/σ(I): 8.4 / Num. measured all: 41029
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 1 % / Num. unique obs: 1746 / % possible all: 79.4

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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: 1ZBL

1zbl


Resolution: 1.324→33.89 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.2
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1715 2006 4.89 %
Rwork0.1483 --
obs0.1495 41027 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.2 Å2 / Biso mean: 27.6723 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: final / Resolution: 1.324→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 47 212 1613
Biso mean--55.75 40.26 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081491
X-RAY DIFFRACTIONf_angle_d1.0592052
X-RAY DIFFRACTIONf_chiral_restr0.07226
X-RAY DIFFRACTIONf_plane_restr0.007212
X-RAY DIFFRACTIONf_dihedral_angle_d21.937591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3245-1.35760.28791210.32132451257283
1.3576-1.39430.32081440.28772711285593
1.3943-1.43530.26491380.25642723286193
1.4353-1.48160.22781490.22182716286593
1.4816-1.53460.21181420.19592719286194
1.5346-1.5960.19581280.1722792292094
1.596-1.66870.18941540.16252789294395
1.6687-1.75670.16371240.15432802292695
1.7567-1.86670.17871260.15922872299896
1.8667-2.01080.19691430.15272812295596
2.0108-2.21310.16681510.14752854300597
2.2131-2.53330.16791600.14382867302797
2.5333-3.19130.17751630.14262914307798
3.1913-33.90230.14081630.12072999316298
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)
16.6020.1039-1.43287.53952.99373.29650.1380.8910.2756-0.7076-0.325-0.6071-0.00671.46670.12250.21180.0910.05690.50160.04250.27340.4779-4.276918.7267
22.07151.48411.8391.94451.58492.19290.11370.1975-0.0598-0.1647-0.1220.11550.13830.0342-0.0320.19510.01910.00520.1769-0.00350.167421.3681-6.273116.2548
39.3245-0.76566.38180.7095-0.85935.84050.35190.2007-0.573-0.1665-0.11140.09640.22690.0653-0.2980.19660.00970.00750.1492-0.0180.180117.82-6.579316.6481
45.5726-3.0984-6.72315.65782.01978.8826-0.1893-0.2456-0.97410.1140.0191-0.24440.55220.4070.1740.22130.03780.0080.17140.02030.291127.8477-11.653623.8565
59.2396-1.85242.91358.9164-6.46645.79370.0085-0.355-0.4804-0.07390.33760.45170.099-0.7415-0.39080.1474-0.00010.01640.1744-0.03830.130810.2097-4.933618.533
65.6985-0.7195.26871.1608-0.34157.7679-0.0229-0.19280.06220.011-0.06850.0477-0.0677-0.29010.09270.11180.0090.03390.09110.0010.123920.96660.587623.957
75.2926-1.07924.58551.96840.36115.30610.0726-0.08450.091-0.001-0.0542-0.05250.1251-0.0434-0.0220.1062-0.00710.02760.1160.00090.122730.7499-1.018525.3954
86.885-6.2673-0.44017.12122.5946.68980.27050.07220.3587-0.2508-0.0845-0.3224-0.69530.1098-0.17560.2668-0.0140.05610.12970.03260.186323.72019.420716.7141
97.1944-1.37252.38752.2974-0.00026.4105-0.00080.07540.351-0.3421-0.31650.5368-0.5357-0.7990.2390.27130.15280.01830.2876-0.05550.20348.54577.733916.1097
105.55333.31444.95623.42063.39844.53860.217-0.20290.09740.0659-0.28440.1287-0.1794-0.50740.10240.19940.05720.02490.242-0.01330.179212.245.69824.8432
114.2784-4.7047-1.1768.75425.08684.78760.2446-0.15350.3642-0.22080.0656-0.3303-0.50080.2137-0.20630.1964-0.01120.01370.13970.02220.160326.24098.315330.3453
122.35490.04620.83195.3795.31497.88820.19850.6162-0.0679-0.5118-0.1494-0.3366-0.09450.4371-0.16390.22230.06010.06620.32120.03160.170634.2705-0.86812.2619
138.96713.1399-3.74394.15350.7583.31860.20980.1912-0.5352-0.134-0.15340.28310.3110.22050.14680.24910.07180.00320.213-0.04510.187626.6044-9.327112.8269
145.49242.16582.2872.1670.26071.4893-0.12840.46340.1801-0.4351-0.0361-0.16790.00240.15250.20190.28420.0730.0520.24550.01310.170523.63720.88985.0501
152.1586-1.2748-1.89355.69853.01043.32480.00780.3327-0.1026-0.8521-0.29580.0243-0.5126-0.12330.37490.3620.0667-0.0180.21640.02110.145516.4193.78643.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:66 )A61 - 66
2X-RAY DIFFRACTION2( CHAIN A AND RESID 67:75 )A67 - 75
3X-RAY DIFFRACTION3( CHAIN A AND RESID 76:87 )A76 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:96 )A88 - 96
5X-RAY DIFFRACTION5( CHAIN A AND RESID 97:104 )A97 - 104
6X-RAY DIFFRACTION6( CHAIN A AND RESID 105:122 )A105 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:133 )A123 - 133
8X-RAY DIFFRACTION8( CHAIN A AND RESID 134:142 )A134 - 142
9X-RAY DIFFRACTION9( CHAIN A AND RESID 143:155 )A143 - 155
10X-RAY DIFFRACTION10( CHAIN A AND RESID 156:169 )A156 - 169
11X-RAY DIFFRACTION11( CHAIN A AND RESID 170:177 )A170 - 177
12X-RAY DIFFRACTION12( CHAIN A AND RESID 178:186 )A178 - 186
13X-RAY DIFFRACTION13( CHAIN A AND RESID 187:194 )A187 - 194
14X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
15X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
16X-RAY DIFFRACTION15( CHAIN C AND RESID 1:6 )C1 - 6

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