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

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Basic information

Entry
Database: PDB / ID: 6dol
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 2)
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
  • 5'-R(P*CP*G)-3' portion of intact 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 / 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 / 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: 1.433 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.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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')
b: 5'-R(P*CP*G)-3' portion of intact 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)20,07615
Polymers19,2424
Non-polymers83411
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-38 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.801, 37.113, 62.105
Angle α, β, γ (deg.)90.000, 96.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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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 intact 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 intact 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: 15587.549 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 61-196)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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, 212 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.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.45 Å3/Da / Density % sol: 49.77 % / Mosaicity: 0 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 20% glycerol, 200 mM potassium iodide, 5 mM calcium chloride

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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: Feb 15, 2016
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→20.06 Å / Num. obs: 33645 / % possible obs: 98.2 % / Redundancy: 1 % / Biso Wilson estimate: 21.48 Å2 / Net I/σ(I): 5.7 / Num. measured all: 33645
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.43-1.4611327179.6
7.85-20.061208190.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZBL

1zbl


Resolution: 1.433→20.06 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.26
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.185 1644 4.89 %
Rwork0.1514 --
obs0.1531 33630 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.24 Å2 / Biso mean: 33.564 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 1.433→20.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 243 37 201 1581
Biso mean--68.43 46.28 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071462
X-RAY DIFFRACTIONf_angle_d1.0022022
X-RAY DIFFRACTIONf_chiral_restr0.069220
X-RAY DIFFRACTIONf_plane_restr0.006212
X-RAY DIFFRACTIONf_dihedral_angle_d24.137575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4326-1.47480.32311040.31312362246687
1.4748-1.52240.32311430.27222614275798
1.5224-1.57670.26531370.23552670280798
1.5767-1.63980.23211530.20532650280398
1.6398-1.71440.22691310.18762653278499
1.7144-1.80480.22981280.17612695282399
1.8048-1.91780.2461500.20052678282899
1.9178-2.06570.19021480.17242696284499
2.0657-2.27330.1921350.15552690282599
2.2733-2.60170.18331400.145427292869100
2.6017-3.27550.17151210.138927632884100
3.2755-20.06280.15021540.11972786294099
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)
14.9884-1.1146-4.15089.3546-0.76034.69530.2060.56760.0431-0.5221-0.4223-0.83430.14541.9930.2550.22530.09630.04430.5630.03180.343140.9071-4.238618.8538
29.703-2.27896.5051.4715-1.7874.54510.42160.1711-0.5843-0.2262-0.11380.12780.487-0.0625-0.35130.208-0-0.0090.2099-0.00240.230919.6058-6.44416.5121
37.4199-1.0168-5.75122.10220.76825.0289-0.0403-0.4271-1.4190.04530.0073-0.38570.69510.2990.1140.24740.0396-0.01380.25220.04130.37828.0986-11.53623.9651
44.753-0.29083.16860.961-0.0054.90660.0619-0.3524-0.0988-0.0137-0.03520.05380.0389-0.3797-0.0260.11890.01370.02730.14350.00350.16222.1003-0.949123.3185
56.9276-3.69651.97945.83611.6043.20740.09540.1440.7533-0.0556-0.2359-0.3529-1.05540.07040.11430.3097-0.00560.00950.15310.03670.249824.10429.341416.5954
68.876-0.56262.89872.1995-2.22225.0290.2035-0.24740.4922-0.0414-0.31740.4767-0.4812-1.04450.0770.32940.2230.00390.4191-0.09760.25548.88317.805316.0409
78.920.50027.59292.43261.10076.91960.1492-0.4554-0.04720.0617-0.18020.0901-0.1902-0.82970.07780.19820.08290.03790.3326-0.03340.199312.59845.724524.8562
85.1111-4.8264-5.06924.54264.90136.3324-0.0146-0.92570.84890.03590.3682-0.5309-0.44190.4592-0.27220.25720.01980.00020.2489-0.04760.267227.11838.340930.4558
93.6971-0.874-0.68067.14234.73183.85860.28910.75140.0025-0.6775-0.197-0.7434-0.04830.6828-0.21170.24110.08020.09070.39650.04840.244834.6774-0.891912.3129
103.35842.0463-4.61848.0991-0.0117.43410.1060.9268-0.3885-0.508-0.11280.37250.7795-0.15040.00890.3480.0821-0.03280.2962-0.06320.280425.4963-9.472612.3434
115.0465-0.38862.86151.9306-2.11544.82190.03390.5422-0.0654-0.6936-0.3399-0.28150.18330.37120.27350.33650.08630.05180.27850.00590.204723.89371.19074.5362
125.0469-0.1225-1.27725.61773.73439.812-0.0440.3617-0.2225-1.1212-0.38850.2348-0.3896-0.42060.4270.39770.1199-0.0110.21620.0060.1816.54383.67133.2369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )A61 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 87 )A67 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 96 )A88 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 133 )A97 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 142 )A134 - 142
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )A143 - 155
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 169 )A156 - 169
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 177 )A170 - 177
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 186 )A178 - 186
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 195 )A187 - 196
11X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4)) or (chain 'b' and (resid 5 through 6))B1 - 4
12X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4)) or (chain 'b' and (resid 5 through 6))b5 - 6
13X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )C1 - 6

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