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

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Basic information

Entry
Database: PDB / ID: 6dpf
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 40 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Components
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • RNA (5'-R(*AP*CP*AP*U)-3') portion of cleaved RNA
  • RNA (5'-R(P*CP*G)-3') portion of cleaved RNA
  • 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 / : / : / TRIETHYLENE GLYCOL / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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') portion of cleaved RNA
b: RNA (5'-R(P*CP*G)-3') portion of cleaved RNA
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,99423
Polymers19,3714
Non-polymers1,62319
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-35 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.726, 37.610, 61.195
Angle α, β, γ (deg.)90.000, 96.200, 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') portion of cleaved RNA


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


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 15716.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (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 (others)

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Non-polymers , 7 types, 186 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-IOD / IODIDE ION


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


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe RNA chain B was split into 2 chains (B and b)
Sequence detailsThe RNA chain B was split into 2 chains (B and b) at the position 4-5, where the cleavage occurs

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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: 2.41 Å3/Da / Density % sol: 48.91 % / 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: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→19.92 Å / Num. obs: 25955 / % possible obs: 97 % / Redundancy: 1 % / Biso Wilson estimate: 22.37 Å2 / Net I/σ(I): 4.1 / Num. measured all: 25955
Reflection shellResolution: 1.56→1.58 Å / Redundancy: 1 % / Num. unique obs: 981 / % possible all: 74.6

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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: 1ZBL

1zbl


Resolution: 1.56→19.92 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.6
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.2068 1285 4.95 %
Rwork0.1623 --
obs0.1644 25946 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.2 Å2 / Biso mean: 33.9396 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 1.56→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 55 167 1576
Biso mean--59.98 41.66 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081466
X-RAY DIFFRACTIONf_angle_d1.0442020
X-RAY DIFFRACTIONf_chiral_restr0.056219
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d18.948831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5563-1.61860.30611130.27252457257087
1.6186-1.69220.2891430.25242743288698
1.6922-1.78130.25571440.23072756290098
1.7813-1.89290.25961470.22092785293299
1.8929-2.03890.23611330.18772795292899
2.0389-2.24380.19911530.17132771292499
2.2438-2.56790.21351460.16952790293699
2.5679-3.23310.21561660.15972762292898
3.2331-19.92530.16751400.12572802294296
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)
12.68810.5427-3.22274.2562-3.92017.46740.30350.4177-0.0319-0.455-0.6194-1.068-0.22662.50380.37860.30560.05940.03480.63390.04130.373240.8951-4.147718.2881
25.2866-0.63074.74371.1623-0.55334.17010.18990.2275-0.4202-0.1268-0.07160.04690.19960.0335-0.24820.21310.0167-0.01710.2218-0.01780.170519.5265-6.260716.0512
36.2934-0.6797-6.91945.53930.92698.4555-0.1756-0.0328-1.61960.1826-0.0222-0.23140.73180.35180.25930.29290.0839-0.02880.20970.04080.345828.238-11.594223.4419
44.3132-1.90332.03495.7592-6.08436.4332-0.0073-0.361-0.168-0.16560.4330.38660.286-1.0747-0.49410.253-0.0203-0.020.3204-0.0220.214810.5097-4.931818.2303
56.6274-1.38575.39132.8601-0.3027.70560.007-0.1394-0.00460.0684-0.08030.0399-0.1566-0.20450.05370.1399-0.00630.020.1578-0.00340.171521.32980.584123.5928
64.6753-1.85922.83331.9627-0.07786.68340.09850.09590.2014-0.0923-0.1005-0.15-0.21630.1903-0.00060.1587-0.04860.02610.1590.02490.169727.95273.670221.1197
73.68432.04693.54461.75970.85155.1711-0.1686-0.09480.705-0.2793-0.37940.5346-0.84-0.71140.39620.43080.2176-0.030.4217-0.06750.283911.33259.552915.7203
85.08410.12273.64395.44030.28016.15480.1702-0.31170.0046-0.054-0.35410.4554-0.0007-0.91390.19290.20920.05530.01980.3528-0.05820.205410.47785.02223.0046
96.1904-4.2818-1.57444.28133.60065.11230.0995-0.46180.4387-0.07310.208-0.3936-0.36390.4174-0.30880.2301-0.00990.01160.21-0.00590.211926.67768.310629.8828
101.9910.17441.27354.94444.72445.09480.24420.39590.032-0.4613-0.1497-0.48390.05350.4576-0.02680.28270.0620.04760.34910.03570.209634.5827-0.827111.864
114.53294.9683-1.6678.6082.98487.9037-0.05430.37-0.0707-0.27340.0810.30150.22780.1248-0.03170.28060.0953-0.03230.2506-0.02980.222325.2947-9.588811.0867
121.9236-1.95722.50896.8496-1.15163.74110.10920.32880.1736-0.585-0.3738-0.34320.00130.19470.27560.30110.09060.04380.33350.02150.16623.94951.24784.284
131.6105-0.8279-2.25494.47132.67583.7374-0.03950.1891-0.0474-0.8686-0.27230.247-0.7843-0.23660.31740.47730.0837-0.05550.32250.01640.179116.49463.59792.9387
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 97:104 )A97 - 104
5X-RAY DIFFRACTION5( CHAIN A AND RESID 105:122 )A105 - 122
6X-RAY DIFFRACTION6( CHAIN A AND RESID 123:142 )A123 - 142
7X-RAY DIFFRACTION7( CHAIN A AND RESID 143:152 )A143 - 152
8X-RAY DIFFRACTION8( CHAIN A AND RESID 153:169 )A153 - 169
9X-RAY DIFFRACTION9( CHAIN A AND RESID 170:177 )A170 - 177
10X-RAY DIFFRACTION10( CHAIN A AND RESID 178:186 )A178 - 186
11X-RAY DIFFRACTION11( CHAIN A AND RESID 187:196 )A187 - 196
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
13X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
14X-RAY DIFFRACTION13( CHAIN C AND RESID 1:6 )C1 - 6

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