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

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Basic information

Entry
Database: PDB / ID: 6doq
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 120 s at 21 C (dataset 2)
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 / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / TRIETHYLENE GLYCOL / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.422 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 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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)21,33120
Polymers19,9854
Non-polymers1,34616
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-32 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.377, 37.862, 61.835
Angle α, β, γ (deg.)90.000, 96.020, 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 RNA (5'-R(*AP*CP*AP*U)-3')


Mass: 1224.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*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
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.) synthetic construct (others)

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Non-polymers , 7 types, 194 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.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 49.58 % / 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: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→19.85 Å / Num. obs: 35113 / % possible obs: 99 % / Redundancy: 1 % / Biso Wilson estimate: 18.34 Å2 / Net I/σ(I): 6.2 / Num. measured all: 35113
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.42-1.4511486185.1
7.79-19.851208187.9

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: pdbid 1ZBL

1zbl


Resolution: 1.422→19.847 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.65
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1768 1726 4.92 %
Rwork0.1489 --
obs0.1503 35107 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.11 Å2 / Biso mean: 30.3493 Å2 / Biso min: 12.66 Å2
Refinement stepCycle: final / Resolution: 1.422→19.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 53 178 1585
Biso mean--57.97 42.92 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081519
X-RAY DIFFRACTIONf_angle_d1.1362083
X-RAY DIFFRACTIONf_chiral_restr0.075231
X-RAY DIFFRACTIONf_plane_restr0.007213
X-RAY DIFFRACTIONf_dihedral_angle_d23.532606
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 (%)
1.4215-1.46340.32341310.30362520265191
1.4634-1.51060.26831460.259528132959100
1.5106-1.56450.24621420.221627732915100
1.5645-1.62720.20321470.189127992946100
1.6272-1.70120.21571570.177327682925100
1.7012-1.79080.20041280.156528222950100
1.7908-1.90290.16121480.153228002948100
1.9029-2.04970.18741620.145427992961100
2.0497-2.25570.17671400.138628092949100
2.2557-2.58150.15721440.144228152959100
2.5815-3.25010.17261290.14312830295999
3.2501-19.84850.15631520.12672833298597
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)
13.40080.89351.46473.70650.70953.02350.11840.67380.0489-0.3658-0.257-0.93020.16761.41270.07830.23950.11590.07790.54920.02860.262340.595-4.38118.697
23.5146-1.56764.54691.7025-1.49096.21420.240.3346-0.2709-0.1974-0.1390.07890.25620.0172-0.12240.19890.00490.00230.2187-0.01090.110619.954-6.21916.603
36.2452.0467-6.21139.07250.18339.2968-0.1325-0.4429-1.16390.17130.0067-0.62380.91120.57580.1070.25560.0737-0.02080.22410.04690.208428.288-11.58423.904
42.9221-0.07091.55170.97580.14013.28590.0754-0.1727-0.0763-0.0344-0.07550.02330.0566-0.18430.00050.16340.01260.02650.18710.00370.086121.773-1.23823.252
54.2799-2.8605-0.3053.77591.91251.88290.27230.29940.3357-0.3051-0.1231-0.3252-0.76350.0456-0.15470.32030.00360.04560.20020.03940.126323.9159.38216.471
67.56981.7191.33082.40581.07185.43060.37690.07930.4207-0.1244-0.59820.4817-0.6957-1.08590.12360.33380.2574-0.01990.4567-0.09410.1868.5967.3916
75.54081.32344.19792.3712.82697.33890.1471-0.2398-0.0053-0.031-0.32870.1523-0.2228-0.74580.17220.20060.06580.01680.2956-0.03640.106812.4865.67924.752
84.4298-4.9988-5.87656.94575.78978.370.1087-0.46760.4467-0.1020.1816-0.3493-0.3440.3359-0.19090.2176-0.0161-0.00590.2347-0.01010.12926.5258.46430.171
91.2017-1.5986-0.68224.25653.96755.7570.16210.44970.0623-0.5857-0.202-0.5159-0.22580.6089-0.19470.26010.08950.1710.48580.04460.013834.724-0.72812.235
102.7646-0.3443-4.70354.67610.0698.0517-0.20840.8828-0.4665-0.8320.00990.22130.8369-0.43970.24520.44740.0431-0.00190.3731-0.08620.144925.369-9.65411.49
112.9466-0.35081.97544.1645-1.00063.28410.04350.3473-0.1399-0.5453-0.2597-0.18920.0660.17990.22530.36950.07390.03480.34020.02570.129423.8160.5415.272
122.2487-1.1797-2.17621.00040.02975.26220.0050.3562-0.1255-0.8224-0.32730.1249-0.2526-0.21180.28110.47190.0986-0.02480.3267-0.01240.137116.4013.4933.104
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 187:196 )A187 - 196
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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