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

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Basic information

Entry
Database: PDB / ID: 6doy
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM Li+ for 120 s at 21 C
Components
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • RNA (5'-R(*AP*CP*AP*UP*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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 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 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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.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.value / _struct_conn.pdbx_dist_value / _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

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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*UP*CP*G)-3')
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,23219
Polymers20,0303
Non-polymers1,20216
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-18 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.898, 37.350, 62.034
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABC

#1: Protein Ribonuclease H / RNase H


Mass: 16330.462 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
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
#2: RNA chain RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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 , 5 types, 204 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION


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


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.44 Å3/Da / Density % sol: 49.64 % / 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: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→19.27 Å / Num. obs: 31921 / % possible obs: 96.1 % / Redundancy: 1 % / Net I/σ(I): 6.5 / Num. measured all: 31921
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.45-1.4711480189.8
7.8-19.271201185.4

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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: 1.45→19.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.1866 1601 5.02 %
Rwork0.148 --
obs0.1499 31904 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 243 50 188 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071469
X-RAY DIFFRACTIONf_angle_d0.9742025
X-RAY DIFFRACTIONf_dihedral_angle_d23.747576
X-RAY DIFFRACTIONf_chiral_restr0.073220
X-RAY DIFFRACTIONf_plane_restr0.006213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4492-1.4960.2981310.30742608X-RAY DIFFRACTION91
1.496-1.54940.32781480.27182685X-RAY DIFFRACTION94
1.5494-1.61140.25761310.21912713X-RAY DIFFRACTION95
1.6114-1.68470.21351600.19212689X-RAY DIFFRACTION95
1.6847-1.77350.22171630.1762719X-RAY DIFFRACTION96
1.7735-1.88450.20341410.16712757X-RAY DIFFRACTION96
1.8845-2.02990.22491480.16422753X-RAY DIFFRACTION97
2.0299-2.23390.17421460.14592797X-RAY DIFFRACTION97
2.2339-2.55650.19081350.14692816X-RAY DIFFRACTION97
2.5565-3.21850.18441450.13912869X-RAY DIFFRACTION98
3.2185-19.27260.15541530.12132897X-RAY DIFFRACTION97
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)
14.1441-0.2945-3.49817.1615-0.79668.31750.37680.43120.0248-0.1698-0.4003-0.6709-0.02011.86660.26890.2310.10450.03980.61260.03230.360640.7425-4.221118.8332
23.3314-0.94435.24461.6214-1.22548.72250.3380.0289-0.409-0.1805-0.1080.11950.4764-0.1941-0.26470.2204-0.0004-0.00450.17750.00160.215119.3167-6.303516.3187
34.7552-0.3563-4.17282.4094-0.01033.71290.1239-0.3609-0.9063-0.04940.0342-0.49290.60590.2836-0.06040.26960.0204-0.01510.25430.02750.356127.1776-11.671423.665
46.1607-1.42832.32263.1417-5.43069.55710.1805-0.6321-0.44480.13480.28810.54710.0739-1.1692-0.42910.2141-0.0491-0.02110.32950.00130.232310.2685-4.987518.4929
54.5909-1.34953.06261.5906-0.37445.830.0144-0.12980.1038-0.0461-0.0661-0.0371-0.1535-0.0920.0340.16210.00260.02560.1314-0.00460.174224.54292.231422.5964
62.3543-1.04891.92762.197-1.51244.79130.2233-0.13710.5058-0.1136-0.40080.5666-0.6002-0.94540.15340.35580.2285-0.02220.4725-0.12480.31818.61387.798416.0032
78.7731.47366.85171.7912.36128.61340.1178-0.35940.0245-0.0531-0.25720.0443-0.3427-0.7640.21380.23820.09880.03190.3076-0.03440.223713.05996.449325.5796
84.7602-2.3887-1.15696.10113.92616.41050.1540.14310.3123-0.2166-0.0388-0.4094-0.06240.3655-0.23250.13220.01190.02060.19830.04210.184832.00472.790620.1345
93.83865.3013-1.85249.77911.39577.1643-0.20210.4218-0.3265-0.66220.00840.10240.8529-0.10750.1140.35510.0812-0.02340.273-0.05080.224225.4888-9.671312.2787
105.53391.49862.66678.7047-0.15483.0488-0.14220.53610.2087-0.7672-0.0017-0.19830.04250.26560.16910.30270.06780.03510.27330.00910.152423.82091.17484.5386
114.5998-0.37280.04495.01671.80155.77620.00490.3267-0.1277-0.8763-0.310.1226-0.3824-0.26410.32930.35740.0927-0.01530.2360.00480.163516.45053.68543.13
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 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 171 )
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 196 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 6 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 6 )

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