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

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Basic information

Entry
Database: PDB / ID: 6dmn
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked in 2 mM Ca2+ and 200 mM K+ 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 / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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 5, 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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: 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)21,04417
Polymers19,9854
Non-polymers1,05913
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-34 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.465, 37.681, 62.022
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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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.) Bacillus halodurans (bacteria)
#3: RNA chain RNA (5'-R(P*CP*G)-3')


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus halodurans (bacteria)

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 16330.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (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.) Bacillus halodurans (bacteria)

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Non-polymers , 6 types, 183 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-IOD / IODIDE ION


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


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.46 Å3/Da / Density % sol: 49.96 % / 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: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→19.864 Å / Num. obs: 46733 / % possible obs: 94.3 % / Redundancy: 3 % / Biso Wilson estimate: 21.27 Å2 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.27-1.2932218190.1
1.29-1.3232303193.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ZBL

1zbl


Resolution: 1.27→19.864 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.09
RfactorNum. reflection% reflection
Rfree0.1714 2369 5.07 %
Rwork0.1501 --
obs0.1512 46730 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.27→19.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 243 32 170 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071461
X-RAY DIFFRACTIONf_angle_d0.9982027
X-RAY DIFFRACTIONf_dihedral_angle_d23.847568
X-RAY DIFFRACTIONf_chiral_restr0.069221
X-RAY DIFFRACTIONf_plane_restr0.007210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.2960.22241470.23582493X-RAY DIFFRACTION91
1.296-1.32410.23841360.2182552X-RAY DIFFRACTION93
1.3241-1.35490.22481470.20572587X-RAY DIFFRACTION93
1.3549-1.38880.21231320.20352562X-RAY DIFFRACTION94
1.3888-1.42640.19091350.18882581X-RAY DIFFRACTION94
1.4264-1.46830.20031180.17942596X-RAY DIFFRACTION94
1.4683-1.51570.17411600.16542602X-RAY DIFFRACTION94
1.5157-1.56980.19971290.15682632X-RAY DIFFRACTION95
1.5698-1.63270.1691380.14862623X-RAY DIFFRACTION95
1.6327-1.70690.15881500.14332654X-RAY DIFFRACTION96
1.7069-1.79690.1591480.14032664X-RAY DIFFRACTION96
1.7969-1.90940.1561500.14982646X-RAY DIFFRACTION97
1.9094-2.05660.15551220.14162727X-RAY DIFFRACTION97
2.0566-2.26340.15141410.13612721X-RAY DIFFRACTION98
2.2634-2.59030.16391440.13982713X-RAY DIFFRACTION97
2.5903-3.26110.17481450.13842718X-RAY DIFFRACTION97
3.2611-19.86670.17481270.15292290X-RAY DIFFRACTION80
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)
14.37052.5781-3.83711.6154-2.19953.45190.32670.4005-0.0115-0.1579-0.1738-0.2436-0.16820.3308-0.2850.20050.11240.02990.48110.01490.269741.1792-3.878419.0153
29.413-1.54085.22971.6879-1.1295.32290.26940.0718-0.4039-0.1001-0.12830.05050.28860.0207-0.19480.17530.00860.00130.1409-0.01030.147219.9434-6.06516.5043
34.6065-4.0161-4.51996.47311.26377.9045-0.0364-0.4929-1.30190.0455-0.0485-0.51130.90810.4326-0.00020.24320.0705-0.02340.17850.07050.348228.2144-11.375323.8093
43.469-0.26522.07640.74250.26973.84440.0428-0.2859-0.0820.0096-0.05090.03390.0516-0.24010.00890.09610.01030.0120.10340.01470.11622.4018-0.979623.6758
57.7373-6.5092-1.40019.01092.76637.8650.0960.11260.5296-0.122-0.0511-0.509-0.77070.2248-0.05580.245-0.01920.00210.11380.03810.172124.1069.516216.5888
64.72330.25320.63762.4797-1.49363.02820.0908-0.42170.4066-0.1567-0.31170.4994-0.5297-1.08710.03010.29760.1812-0.00970.4061-0.09420.21758.80387.815716.0247
73.54750.81984.01282.42641.05125.81010.1034-0.29840.0805-0.068-0.29320.2001-0.1499-0.76380.23470.1530.05270.00130.2586-0.05590.15412.72196.073225.1243
83.8647-5.5743-4.66628.40395.80788.4095-0.0278-0.55570.37720.01720.2438-0.287-0.23780.3124-0.10580.1593-0.0106-0.01180.1838-0.01270.165726.7068.447330.3183
90.745-0.372-0.27877.34825.39764.50910.19630.57230.1343-0.5451-0.1591-0.6583-0.00150.7226-0.20410.22520.0820.0750.40080.03980.189734.811-0.706912.2223
103.74132.1604-4.30353.5711-0.63977.4176-0.0970.5003-0.4732-0.5096-0.1453-0.06790.84160.03650.12710.36650.1033-0.00740.252-0.05260.215326.7882-9.506812.5386
113.3452-0.77931.46856.5663-0.4395.870.08460.2901-0.0537-0.7812-0.3917-0.20960.17650.44620.17420.23020.07840.0260.1790.01840.109323.01930.36814.5184
124.1371-0.4736-0.18754.5462.70749.53970.08060.3803-0.0408-0.7566-0.3150.0788-0.4817-0.20560.26540.29020.0893-0.02510.1760.01070.120916.6343.84083.1441
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 67:87 )A67 - 87
3X-RAY DIFFRACTION3( CHAIN A AND RESID 88:96 )A88 - 96
4X-RAY DIFFRACTION4( CHAIN A AND RESID 97:133 )A97 - 133
5X-RAY DIFFRACTION5( CHAIN A AND RESID 134:142 )A134 - 142
6X-RAY DIFFRACTION6( CHAIN A AND RESID 143:155 )A143 - 155
7X-RAY DIFFRACTION7( CHAIN A AND RESID 156:169 )A156 - 169
8X-RAY DIFFRACTION8( CHAIN A AND RESID 170:177 )A170 - 177
9X-RAY DIFFRACTION9( CHAIN A AND RESID 178:186 )A178 - 186
10X-RAY DIFFRACTION10( CHAIN A AND RESID 187:195 )A187 - 195
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
12X-RAY DIFFRACTION11( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
13X-RAY DIFFRACTION12( CHAIN C AND RESID 1:6 )C1 - 6

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