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

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Basic information

Entry
Database: PDB / ID: 6doz
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 1 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of uncleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • 5'-R(P*CP*G)-3' portion of uncleaved 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 / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.573 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 / 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_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_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_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease H
B: 5'-R(*AP*CP*AP*U)-3' portion of uncleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
b: 5'-R(P*CP*G)-3' portion of uncleaved 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)20,89316
Polymers19,9854
Non-polymers90812
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-37 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.576, 37.475, 62.495
Angle α, β, γ (deg.)90.000, 96.670, 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 uncleaved 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 uncleaved 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: 16330.462 Da / Num. of mol.: 1 / Fragment: Catalytic Domain residues 59-196
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 BL21(DE3) (bacteria) / 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 construct (others)

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Non-polymers , 6 types, 181 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.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-IOD / IODIDE ION


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


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 49.99 % / 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-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→19.36 Å / Num. obs: 25891 / % possible obs: 98.3 % / Redundancy: 1 % / Biso Wilson estimate: 26.89 Å2 / Net I/σ(I): 9.5 / Num. measured all: 25891
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.57-1.61995177.1
8.62-19.361163190.2

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Processing

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

1zbl


Resolution: 1.573→19.36 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.5
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1847 2482 4.94 %
Rwork0.1524 --
obs0.154 50222 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.17 Å2 / Biso mean: 40.1555 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 1.573→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 243 33 169 1545
Biso mean--67.67 47.1 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081448
X-RAY DIFFRACTIONf_angle_d1.0562006
X-RAY DIFFRACTIONf_chiral_restr0.058219
X-RAY DIFFRACTIONf_plane_restr0.007210
X-RAY DIFFRACTIONf_dihedral_angle_d20.184826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.573-1.60330.33681120.29532146225879
1.6033-1.6360.281300.27562537266795
1.636-1.67150.2641380.25582665280398
1.6715-1.71040.27481430.231326552798100
1.7104-1.75310.26441060.212727282834100
1.7531-1.80050.21991360.197627212857100
1.8005-1.85340.22011510.198526952846100
1.8534-1.91320.19511570.183526492806100
1.9132-1.98150.2031380.170127162854100
1.9815-2.06080.20671430.162626642807100
2.0608-2.15450.2091310.158127172848100
2.1545-2.26790.2191000.152727502850100
2.2679-2.40970.18771570.158526682825100
2.4097-2.59540.191440.162226942838100
2.5954-2.85580.18421590.15626942853100
2.8558-3.26730.171420.157726672809100
3.2673-4.110.1851420.127827172859100
4.11-19.36120.1441530.12382657281099
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined5.4244-2.49582.78313.3267-0.77615.34550.47640.2766-0.49-0.1816-0.2199-0.01970.48810.1521-0.32780.25760.02920.02210.1747-0.00360.190925.4604-5.717517.4435
2refined6.5703-2.8801-5.65287.13551.0275.5093-0.0661-0.408-1.5953-0.0885-0.1069-0.37410.79040.2980.23680.3050.0271-0.00380.25250.05870.414727.9907-11.489324.0924
3refined5.5331-0.22723.84531.13550.34565.10660.0863-0.4516-0.1365-0.0248-0.07350.04890.0635-0.5151-0.00410.16420.01070.03320.16250.00160.168321.8835-0.950423.4437
4refined8.4158-5.9306-1.86934.66052.88098.45860.15980.10920.6414-0.2163-0.0888-0.6035-1.3682-0.0506-0.0560.441-0.00790.0180.18150.04820.292623.82829.372816.6824
5refined3.54821.97282.87627.19421.2025.69930.4814-0.08070.7179-0.1003-0.65230.6564-1.0323-1.33360.14110.40120.4207-0.0180.5845-0.16710.27598.55557.405416.3041
6refined8.83443.20716.5332.97332.97935.05260.0674-0.89670.164-0.037-0.34940.0991-0.3858-1.03990.33820.28420.11130.01450.4072-0.06410.238812.29935.681125.0086
7refined4.8011-0.58120.03712.2769-0.02935.45470.13060.444-0.0722-0.2935-0.1031-0.16650.19960.1366-0.1390.22690.03910.02010.20380.02350.19428.982-0.323418.3721
8refined5.5135-0.49473.52074.4498-0.6724.73490.09930.73040.0009-0.5627-0.1912-0.0530.1840.21340.16540.39280.08290.050.35130.00690.228823.74711.29424.6211
9refined4.1459-1.5094-1.92595.49713.92193.8643-0.01650.3307-0.1701-1.2622-0.47680.249-0.8673-0.40350.48730.50310.0978-0.0190.3206-0.00010.200916.36793.68453.2803
10
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 87 )A61 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 96 )A88 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 133 )A97 - 133
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 142 )A134 - 142
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 155 )A143 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 169 )A156 - 169
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 196 )A170 - 196
8X-RAY DIFFRACTION8(chain 'B' and (resid 1 through 4 )) OR (chain 'b' and (resid 5 through 6 ))B1 - 4
10X-RAY DIFFRACTION9chain 'C' and (resid 1 through 6 )C1 - 6
9X-RAY DIFFRACTION8(chain 'B' and (resid 1 through 4 )) OR (chain 'b' and (resid 5 through 6 ))b5 - 6

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