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

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Basic information

Entry
Database: PDB / ID: 6dph
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mn2+ and 200 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/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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.339 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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: 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)21,30521
Polymers19,9274
Non-polymers1,37817
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-28 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.867, 37.063, 61.789
Angle α, β, γ (deg.)90.000, 96.330, 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: 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 , 7 types, 219 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.: 4 / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.42 Å3/Da / Density % sol: 49.17 % / 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 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.339→23.2 Å / Num. obs: 40256 / % possible obs: 97.4 % / Redundancy: 1 % / Biso Wilson estimate: 17.25 Å2 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.34-1.3611339166.1
7.33-23.21241188.2

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ZBL

1zbl


Resolution: 1.339→23.197 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.47
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1918 1977 4.92 %
Rwork0.1595 --
obs0.161 40200 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.65 Å2 / Biso mean: 29.2807 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 1.339→23.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 243 55 202 1581
Biso mean--60.11 40.83 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091458
X-RAY DIFFRACTIONf_angle_d1.0662018
X-RAY DIFFRACTIONf_chiral_restr0.07221
X-RAY DIFFRACTIONf_plane_restr0.006210
X-RAY DIFFRACTIONf_dihedral_angle_d23.336574
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 (%)
1.3386-1.37210.37251210.34912097221875
1.3721-1.40910.29521290.30922591272094
1.4091-1.45060.29051460.26972734288099
1.4506-1.49740.27921370.236728052942100
1.4974-1.55090.22971180.221827962914100
1.5509-1.6130.21471250.183428082933100
1.613-1.68640.21121740.174227592933100
1.6864-1.77530.18711300.169828202950100
1.7753-1.88650.1851550.182727562911100
1.8865-2.0320.20641490.1727912940100
2.032-2.23640.18271560.156627872943100
2.2364-2.55960.17641430.152127962939100
2.5596-3.22350.19951560.147428172973100
3.2235-23.20090.15821380.12592866300498
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)
15.90041.1681-0.2449.18951.60835.67690.06850.63350.05-0.4713-0.1404-1.0340.03961.32320.14050.17690.08450.04480.48710.03580.330440.53-3.95818.782
29.01052.66887.46594.9844.16467.64040.1646-0.3273-0.1031-0.2163-0.23370.23430.1953-0.45930.04820.1408-0.0035-0.00410.17010.03440.126821.983-6.13716.448
38.4258-3.20335.98884.112-2.84454.53440.43860.0623-0.4601-0.2646-0.17030.14330.433-0.0871-0.30340.17160.0018-0.010.1912-0.01460.168817.637-6.20716.41
44.1687-1.8516-4.10117.6023-0.07756.9756-0.1053-0.3928-1.21160.0890.0262-0.31580.69780.317-0.00230.19480.0485-0.01190.16950.03770.265327.211-11.40123.691
57.8578-0.03250.99417.9444-5.69264.24190.0326-0.4691-0.3812-0.03350.40290.66520.1694-1.0526-0.44610.1597-0.0169-0.02010.2681-0.02340.181310.404-4.87918.456
65.574-1.22324.65151.963-0.40816.3355-0.024-0.317-0.0103-0.022-0.03490.0392-0.1362-0.31770.00060.08330.01550.01870.1241-0.00380.123421.0170.67923.817
74.9072-0.75973.85551.27430.5067.29280.0294-0.202-0.00730.0318-0.046-0.05930.1423-0.00930.02260.09220.00210.00580.12970.01480.139930.767-0.84925.251
87.7302-4.3482-2.0113.37611.60367.19280.12290.1760.5378-0.0927-0.1157-0.3416-0.89720.1630.01620.2539-0.0168-0.00480.10210.02880.186123.8728.77416.119
96.3564-0.2541.55670.8673-0.71692.20440.3447-0.06050.4098-0.1473-0.44320.3057-0.9415-0.85460.15990.29150.3304-0.05140.4856-0.08920.2379.6318.15116.324
109.24090.99817.121.78621.11047.14890.1269-0.4675-0.03680.0954-0.29890.0763-0.4517-0.89120.22630.21060.11560.0150.3008-0.0440.177913.0566.42625.509
114.2799-5.0872-5.25036.43875.3828.21370.015-0.72450.62020.11980.2763-0.271-0.18910.4321-0.14610.1476-0.0051-0.00520.2148-0.02730.198928.1657.45529.883
122.8335-1.6184-1.83188.08055.81678.46350.32150.66190.134-0.6527-0.1778-0.7639-0.1010.7139-0.20790.19880.08020.06640.38280.06260.202534.383-0.63212.255
134.49693.4978-5.87336.7178-4.49337.9088-0.1511.3263-0.9931-0.4149-0.14360.10831.0476-0.33890.20970.3180.0687-0.03780.3122-0.10050.258527.204-9.01713.517
145.6399-0.42471.60654.01890.0866.17380.0420.4830.0913-0.6124-0.2794-0.19220.00790.45370.21990.2350.07820.01080.20970.01760.124323.5911.4114.487
153.331-0.2774-1.85087.09312.57952.4861-0.08020.2198-0.0794-0.9016-0.31740.3378-0.6649-0.22180.4040.33670.0937-0.05090.2050.0150.159416.33.8633.12
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 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
15X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
16X-RAY DIFFRACTION15( CHAIN C AND RESID 1:6 )C1 - 6

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