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- PDB-6dpn: Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in... -

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Basic information

Entry
Database: PDB / ID: 6dpn
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 200 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/RNA/DNA / protein-RNA-DNA complex / double helix / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / monovalent cations / divalent cations / HYDROLASE-RNA-DNA 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: 1.493 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_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

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)21,11619
Polymers19,9274
Non-polymers1,18915
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-36 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.501, 37.581, 61.951
Angle α, β, γ (deg.)90.00, 96.24, 90.00
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: 16272.427 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Mutation: E188A
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) / 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, 200 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-IOD / IODIDE ION


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


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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 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: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→19.89 Å / Num. obs: 29802 / % possible obs: 97.7 % / Redundancy: 1 % / Net I/σ(I): 6.6
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 1 % / % possible all: 75.4

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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: PDBID 1ZBL

1zbl


Resolution: 1.493→19.893 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1792 2963 5.11 %
Rwork0.1589 --
obs0.1599 57966 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.493→19.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 243 44 185 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081452
X-RAY DIFFRACTIONf_angle_d1.0162008
X-RAY DIFFRACTIONf_dihedral_angle_d22.304568
X-RAY DIFFRACTIONf_chiral_restr0.07219
X-RAY DIFFRACTIONf_plane_restr0.006209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.493-1.51750.3289990.30972011X-RAY DIFFRACTION74
1.5175-1.54370.32471480.30862625X-RAY DIFFRACTION96
1.5437-1.57170.29341340.27662632X-RAY DIFFRACTION99
1.5717-1.60190.2541330.26442678X-RAY DIFFRACTION99
1.6019-1.63460.28181570.23352606X-RAY DIFFRACTION99
1.6346-1.67010.30331380.22172677X-RAY DIFFRACTION100
1.6701-1.7090.23371720.21642637X-RAY DIFFRACTION99
1.709-1.75170.19271560.1842608X-RAY DIFFRACTION100
1.7517-1.7990.2181580.18322694X-RAY DIFFRACTION99
1.799-1.85190.28611420.18422661X-RAY DIFFRACTION99
1.8519-1.91170.23591540.20142643X-RAY DIFFRACTION99
1.9117-1.97990.21371610.1912643X-RAY DIFFRACTION100
1.9799-2.05910.18241510.16932661X-RAY DIFFRACTION100
2.0591-2.15270.19761390.16462683X-RAY DIFFRACTION99
2.1527-2.26610.19671240.16332657X-RAY DIFFRACTION99
2.2661-2.40780.20221100.162686X-RAY DIFFRACTION99
2.4078-2.59340.16441590.16032658X-RAY DIFFRACTION99
2.5934-2.85370.20221230.15572663X-RAY DIFFRACTION99
2.8537-3.2650.15131310.1472644X-RAY DIFFRACTION99
3.265-4.10760.13541370.12862657X-RAY DIFFRACTION98
4.1076-19.89470.14021370.12562579X-RAY DIFFRACTION97
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)
13.8327-0.3137-1.24663.1145-3.24029.07090.36380.6489-0.0234-0.2253-0.5003-0.6593-0.02891.77510.42120.22370.0990.03350.50240.01880.361541.0023-3.910918.861
22.3847-1.48271.65872.66830.30252.29750.3627-0.0156-0.3525-0.101-0.2118-0.0270.402-0.1071-0.26950.22670.00760.00850.20040.02290.182722.8136-5.890616.7627
36.3732-1.94577.10862.2205-2.47039.70390.27570.2961-0.2786-0.2202-0.21040.06050.3229-0.0329-0.07850.2261-0.0171-0.00480.1883-0.02910.229718.1707-6.618816.6369
45.1543-2.4725-4.7992.58691.68254.759-0.1373-0.3866-0.9219-0.060.1383-0.36040.88950.46780.10150.28580.0594-0.00190.22590.05360.373628.2524-11.472123.8608
56.5226-1.41383.97329.3706-5.82479.88930.0298-0.4831-0.55080.00810.34010.5060.2731-1.4108-0.39360.1888-0.01650.00660.3349-0.01110.222910.55-5.119618.5512
65.2613-0.8375.20651.53880.01467.1421-0.0151-0.3094-0.0092-0.0445-0.04710.0352-0.0911-0.37630.02620.10860.01320.03240.1243-0.00350.160821.20180.611523.8839
73.971-0.91754.10111.0896-0.04588.21060.0575-0.0668-0.0604-0.0399-0.033-0.0550.2510.0298-0.00540.14970.00080.01330.16490.01180.204431.0583-0.843925.3221
86.9312-5.7514-2.22855.2771.43171.75090.25370.19030.4105-0.1955-0.2149-0.3826-0.89960.1903-0.03910.3129-0.01470.01140.13450.03010.220924.0158.768116.1363
94.67472.62953.05263.53010.42412.84120.3739-0.3660.5589-0.1123-0.60060.4517-0.6316-0.84950.25410.35440.2822-0.01440.4747-0.14190.30039.57467.764916.4296
105.10382.29185.23292.68292.68245.44120.0405-0.34140.17190.0546-0.2590.1518-0.2373-0.68220.26280.23140.08050.01810.3009-0.04060.215213.1286.338325.5882
114.3522-4.41160.43118.01823.82329.09390.0728-0.76650.7728-0.09520.3022-0.5686-0.21460.6463-0.33820.1646-0.0220.00020.1537-0.05750.234128.91737.576330.1471
124.4849-1.0681-0.41677.48485.31694.02630.30350.8654-0.0935-0.663-0.2858-0.5444-0.13390.5024-0.11930.27250.08950.06660.4040.03510.218734.7444-0.631512.2695
134.2659-0.5901-6.00496.3712-0.58018.8387-0.23780.3873-0.7818-0.4810.06980.04511.26070.08510.13780.35820.0822-0.01020.2497-0.06130.252827.501-9.032413.5893
145.2361-0.17222.92479.4095-0.30593.4594-0.11430.453-0.1119-0.8636-0.1456-0.20880.24930.26930.26580.3430.05550.03240.28010.00990.178823.83421.32334.5181
152.8563-2.1695-2.61923.73481.7175.5660.02420.3447-0.1202-1.0423-0.42280.2174-0.6154-0.2390.39330.44810.0968-0.02680.22850.00280.184716.43.63153.1745
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 67:75 )A67 - 75
3X-RAY DIFFRACTION3( CHAIN A AND RESID 76:87 )A76 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:96 )A88 - 96
5X-RAY DIFFRACTION5( CHAIN A AND RESID 97:104 )A97 - 104
6X-RAY DIFFRACTION6( CHAIN A AND RESID 105:122 )A105 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:133 )A123 - 133
8X-RAY DIFFRACTION8( CHAIN A AND RESID 134:141 )A134 - 141
9X-RAY DIFFRACTION9( CHAIN A AND RESID 142:155 )A142 - 155
10X-RAY DIFFRACTION10( CHAIN A AND RESID 156:171 )A156 - 171
11X-RAY DIFFRACTION11( CHAIN A AND RESID 172:177 )A172 - 177
12X-RAY DIFFRACTION12( CHAIN A AND RESID 178:186 )A178 - 186
13X-RAY DIFFRACTION13( CHAIN A AND RESID 187:193 )A187 - 193
14X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 )B1 - 4
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1:6 )C1 - 6

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