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- PDB-6dpk: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in... -

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Basic information

Entry
Database: PDB / ID: 6dpk
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 4 mM Mn2+ and 200 mM K+ for 240 s at 21 C
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • 5'-R(P*CP*G)-3' portion of cleaved 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


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 / Resolution: 1.391 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.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_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.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 cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
b: 5'-R(P*CP*G)-3' portion of cleaved 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)21,28422
Polymers19,9274
Non-polymers1,35718
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-30 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.492, 37.598, 61.734
Angle α, β, γ (deg.)90.000, 96.790, 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 cleaved 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 cleaved 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: 16272.360 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Mutation: K196A
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, 207 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-IOD / IODIDE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.43 Å3/Da / Density % sol: 49.48 % / 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: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→19.92 Å / Num. obs: 37271 / % possible obs: 99.3 % / Redundancy: 1 % / Biso Wilson estimate: 17.01 Å2 / Net I/σ(I): 6.7 / Num. measured all: 37271
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.39-1.4211769192.9
7.49-19.921225186

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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: 1.391→19.92 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.52
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1685 1904 5.11 %
Rwork0.1434 --
obs0.1446 37254 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.17 Å2 / Biso mean: 27.7889 Å2 / Biso min: 12.08 Å2
Refinement stepCycle: final / Resolution: 1.391→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 244 53 189 1586
Biso mean--63.63 41.13 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081555
X-RAY DIFFRACTIONf_angle_d1.0882133
X-RAY DIFFRACTIONf_chiral_restr0.071234
X-RAY DIFFRACTIONf_plane_restr0.007217
X-RAY DIFFRACTIONf_dihedral_angle_d22.773618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.391-1.42570.31370.30842345248294
1.4257-1.46430.24951450.25642505265099
1.4643-1.50730.251270.20725562683100
1.5073-1.5560.21521420.187324612603100
1.556-1.61160.17931100.170925742684100
1.6116-1.67610.18841150.155225602675100
1.6761-1.75230.16451340.14225012635100
1.7523-1.84460.18181520.139925252677100
1.8446-1.96010.20861430.147725412684100
1.9601-2.11130.15451400.137125362676100
2.1113-2.32350.14431440.13632525266999
2.3235-2.6590.15111460.13132532267899
2.659-3.34750.17721360.136125632699100
3.3475-19.92680.14551330.12762626275999
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)
15.27320.1081-1.91422.851.25368.12030.23860.63650.209-0.2347-0.2196-0.7692-0.00371.71150.1340.20750.08070.01690.54360.04280.283440.572-4.23718.69
25.511-0.17022.78431.7063-0.04725.09140.22010.0173-0.3546-0.0952-0.07210.05230.3043-0.0817-0.18110.1781-0.0013-0.01910.1273-0.00050.137819.329-6.40216.299
39.48721.1677-2.42755.0687-0.08466.00610.0862-0.1606-1.17860.0752-0.1084-0.37020.62750.22460.01820.25130.0346-0.04180.17280.02850.254727.061-11.64123.53
43.37730.16420.58275.9884-3.12556.1504-0.0434-0.2384-0.1804-0.04690.24270.40890.204-0.7819-0.14850.176-0.0214-0.01030.28940.00080.168510.148-5.39918.852
53.3695-0.02642.2061.43770.88485.342-0.0084-0.1637-0.00420.045-0.04630.0534-0.0866-0.14270.02520.11070.0030.00440.12610.00310.116620.9780.65123.783
62.7981-0.32511.59832.06110.24736.63150.0376-0.159-0.01640.0456-0.0039-0.0530.09310.0441-0.04160.11790.0075-0.00280.17430.01140.13830.762-0.95325.218
75.3076-4.2233-1.11785.31592.71932.09140.33440.17560.3107-0.3437-0.1771-0.321-0.6237-0.0068-0.17180.2631-0.00350.0050.15090.03220.158523.7169.46816.542
87.1212-0.82781.74951.6689-1.09534.97470.1894-0.0310.4384-0.1508-0.28390.454-0.4762-0.89280.12020.26910.1568-0.00670.3407-0.04090.1978.5237.87515.838
96.30490.88563.71152.37341.32956.98950.1707-0.18050.06030.0386-0.1990.1638-0.0808-0.59860.04060.17110.04910.00730.2335-0.01860.145112.2725.76824.672
103.7117-3.9777-4.99625.60453.95468.27640.146-0.42510.4109-0.06030.1282-0.1816-0.43070.2249-0.17970.1855-0.0059-0.01470.1831-0.00940.158426.298.3830.154
112.0656-1.08180.20127.17684.50583.42320.21770.49780.0105-0.4512-0.1782-0.4869-0.08220.4783-0.09580.20390.0540.0380.32950.03010.152834.35-0.8212.155
122.7661-0.9214-3.27972.9145-0.77475.2389-0.10010.5999-0.4903-0.28350.01640.03570.60160.007-0.04410.26430.0484-0.0250.2205-0.05020.167225.797-9.68112.566
133.19640.02471.40584.6244-0.05324.08690.0080.21120.0181-0.4849-0.2114-0.19060.01030.2140.16010.26050.07040.00290.2260.01560.118723.8580.75.244
142.3835-0.6568-0.30623.19541.48424.56930.04690.1604-0.0714-0.7766-0.31370.133-0.465-0.22990.29870.35830.0764-0.04550.21120.01030.144216.4113.8333.089
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 123:133 )A123 - 133
7X-RAY DIFFRACTION7( CHAIN A AND RESID 134:142 )A134 - 142
8X-RAY DIFFRACTION8( CHAIN A AND RESID 143:155 )A143 - 155
9X-RAY DIFFRACTION9( CHAIN A AND RESID 156:169 )A156 - 169
10X-RAY DIFFRACTION10( CHAIN A AND RESID 170:177 )A170 - 177
11X-RAY DIFFRACTION11( CHAIN A AND RESID 178:186 )A178 - 186
12X-RAY DIFFRACTION12( CHAIN A AND RESID 187:195 )A187 - 195
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
14X-RAY DIFFRACTION13( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
15X-RAY DIFFRACTION14( CHAIN C AND RESID 1:6 )C1 - 6

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