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

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Basic information

Entry
Database: PDB / ID: 6doj
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 5 mM K+ for 120 s at 21 C
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


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 construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.403 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)20,13517
Polymers19,2424
Non-polymers89313
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-28 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.873, 37.361, 62.275
Angle α, β, γ (deg.)90.000, 96.710, 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 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, 216 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.: 1 / 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 49.84 % / 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: 1.4→20.02 Å / Num. obs: 36467 / % possible obs: 98.9 % / Redundancy: 1 % / Biso Wilson estimate: 20.27 Å2 / Net I/σ(I): 5.8 / Num. measured all: 36467
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.4-1.4311473181.6
7.68-20.021223189.1

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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: PDB entry 1ZBL

1zbl


Resolution: 1.403→20.018 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.73
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1846 1797 4.93 %
Rwork0.1449 --
obs0.1469 36463 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.81 Å2 / Biso mean: 32.5861 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 1.403→20.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 243 48 203 1594
Biso mean--56.89 46.26 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071462
X-RAY DIFFRACTIONf_angle_d1.0672018
X-RAY DIFFRACTIONf_chiral_restr0.072219
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d24.556572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.403-1.44090.3513940.32482387248188
1.4409-1.48330.28911620.26622629279199
1.4833-1.53110.23881290.228826352764100
1.5311-1.58580.20041400.202326832823100
1.5858-1.64930.25711310.186327042835100
1.6493-1.72430.19351600.16826662826100
1.7243-1.81520.18741480.162526732821100
1.8152-1.92880.22671500.157726652815100
1.9288-2.07760.16331460.144626962842100
2.0776-2.28640.1851310.138126912822100
2.2864-2.61660.1871280.142127302858100
2.6166-3.29430.18011430.137827252868100
3.2943-20.02020.1611350.12012782291799
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)
14.94880.9268-4.98499.4141-1.74427.6280.15090.47490.063-0.3157-0.3675-0.67690.28121.85430.28870.17030.07780.02380.52170.0250.284440.7827-4.279418.9327
28.6665-1.20364.94571.0066-1.02045.28410.42490.0096-0.546-0.2008-0.09810.09840.4201-0.1609-0.36720.21620.0014-0.02310.1413-0.00180.225719.347-6.29716.4517
36.243-0.4928-5.2867.1118-0.08395.0414-0.0371-0.6117-1.50810.0616-0.0217-0.53530.81480.37220.07550.2860.028-0.04880.22810.05830.373227.9347-11.580424.0347
45.0879-0.33293.16660.8261-0.00484.43970.0683-0.4121-0.0702-0.0236-0.04890.05330.0603-0.3952-0.01210.12910.01060.02150.12550.00540.150721.978-0.957523.3538
58.1743-5.6219-0.68364.34051.79638.31840.24560.13150.5475-0.0986-0.1668-0.5956-1.06640.2345-0.05650.3182-0.00570.01350.12690.03720.235624.03979.364716.619
67.29771.66373.97066.1091.21968.50790.2732-0.14340.38710.0705-0.36810.5495-0.3868-1.06230.10720.29510.225-0.00150.3561-0.09190.23218.75697.725116.2029
77.30322.08275.6672.17751.86784.52770.1394-0.44140.02760.0273-0.22480.0499-0.2999-0.77380.12540.22970.09070.00630.3276-0.04560.222712.48935.784324.9192
84.9767-5.8602-6.59338.1426.81459.51120.1471-0.68130.714-0.12360.2991-0.4865-0.4730.3951-0.24040.21980.0082-0.01180.208-0.02950.227727.03148.352430.5332
93.18970.05370.74014.36564.38314.85190.35790.7907-0.0595-0.4637-0.1946-0.6262-0.02890.4737-0.25260.2510.08340.07640.35790.04040.235934.6311-0.963812.3408
105.73362.4347-5.18864.9216-1.33584.92180.09540.74-0.5465-0.46630.03270.24270.699-0.1422-0.06390.36980.079-0.0420.2449-0.06560.291625.5009-9.45812.5204
113.9124-0.75682.83898.8269-2.2334.58020.09890.5275-0.0976-0.8241-0.3959-0.35390.17180.37480.27820.3250.09530.05350.27290.00830.178823.85931.21594.5603
124.6624-0.7967-1.18255.67443.45884.62640.05130.3423-0.2205-1.0535-0.37230.1527-0.6632-0.3160.34020.38470.0906-0.02810.21650.00370.164216.50163.67053.2427
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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