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

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Basic information

Entry
Database: PDB / ID: 6dpa
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 4 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


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 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 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: 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)20,56819
Polymers19,3714
Non-polymers1,19715
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-29 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.199, 37.746, 62.051
Angle α, β, γ (deg.)90.000, 96.250, 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 , 6 types, 184 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / 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


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.: 3 / 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.: 169 / 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)
Source 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: 2.47 Å3/Da / Density % sol: 50.22 % / 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: 1.49→19.83 Å / Num. obs: 30236 / % possible obs: 98.2 % / Redundancy: 1 % / Biso Wilson estimate: 19.21 Å2 / Net I/σ(I): 6.1 / Num. measured all: 30236
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 1 % / Num. measured all: 1388 / Num. unique obs: 1388 / Net I/σ(I) obs: 1.1 / % possible all: 90.3

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Processing

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

1zbl


Resolution: 1.489→19.827 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.53 / Stereochemistry target values: ML
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1863 1530 5.06 %
Rwork0.1549 28699 -
obs0.1564 30229 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.49 Å2 / Biso mean: 29.8236 Å2 / Biso min: 11.91 Å2
Refinement stepCycle: final / Resolution: 1.489→19.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 244 39 169 1541
Biso mean--54.14 42.33 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081466
X-RAY DIFFRACTIONf_angle_d1.0832030
X-RAY DIFFRACTIONf_chiral_restr0.073225
X-RAY DIFFRACTIONf_plane_restr0.006209
X-RAY DIFFRACTIONf_dihedral_angle_d22.769583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4891-1.53720.29711250.28982455258093
1.5372-1.59210.27121420.24442536267897
1.5921-1.65580.25321420.21962604274697
1.6558-1.73110.23881120.19872597270997
1.7311-1.82230.24491380.1862584272298
1.8223-1.93640.20021640.17662596276099
1.9364-2.08570.18531360.15662631276799
2.0857-2.29540.19881440.14532617276199
2.2954-2.62690.17531530.15092647280099
2.6269-3.30710.16761500.148326762826100
3.3071-19.8290.15771240.12852756288099
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)
13.5476-0.89971.88471.65040.10152.64050.27320.371-0.1482-0.1366-0.1947-0.12640.30980.3214-0.05270.18250.01490.03350.18150.0220.136625.0698-5.849517.0932
25.8838-1.7325-5.7738.45041.84916.8073-0.0607-0.523-1.0015-0.00690.0129-0.840.71010.46560.17040.26880.06360.02430.19810.06870.328728.0489-11.511223.9184
32.3289-3.4683.64166.0944-5.31915.9280.129-0.4717-0.4635-0.0510.30.46820.207-0.8918-0.48190.1885-0.03140.00370.2885-0.00690.167210.4467-5.085718.5733
44.163-1.09712.4591.3286-0.00163.9540.0059-0.0620.1174-0.0391-0.0537-0.0339-0.1762-0.0336-0.00530.1427-0.00480.04470.09010.0040.117824.59422.120522.5749
58.11251.26541.53833.56670.84085.35530.2974-0.00480.4167-0.1424-0.62120.5112-0.6916-1.06510.24380.33830.2115-0.00710.3596-0.1120.21659.55957.926516.3695
67.85571.64446.46761.81252.72888.57540.1648-0.3093-0.0902-0.0352-0.20730.1187-0.2226-0.72480.11450.16160.05470.02950.2235-0.03460.1512.35475.701324.8585
74.7505-4.84-5.60624.975.72886.6440.1723-0.40020.699-0.21910.1979-0.5049-0.34970.4159-0.29640.1987-0.00870.03280.1837-0.00510.183926.37178.422630.299
82.14770.81680.0136.84594.42773.6070.18780.651-0.0598-0.7206-0.2124-0.51380.14540.6043-0.11280.30680.10490.09030.37350.04550.184634.4906-0.684212.2962
92.38210.8884-1.22951.4495-0.30041.3406-0.02470.6012-0.1745-0.37280.07760.23270.8612-0.21340.22830.38490.01570.02790.3562-0.06290.214926.0473-8.042912.0106
103.8742-0.57933.32777.7082-0.5483.1457-0.03840.48680.0105-0.7144-0.1631-0.35310.01880.22030.24030.29330.06260.06360.23010.00430.129623.6990.87194.9703
112.6295-1.4766-1.42311.86343.21589.27310.07580.2979-0.1403-0.7941-0.38410.0502-0.4174-0.2660.31920.41920.0871-0.01440.2002-0.0010.152816.36143.56693.1858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:87 )A61 - 87
2X-RAY DIFFRACTION2( CHAIN A AND RESID 88:96 )A88 - 96
3X-RAY DIFFRACTION3( CHAIN A AND RESID 97:104 )A97 - 104
4X-RAY DIFFRACTION4( CHAIN A AND RESID 105:141 )A105 - 141
5X-RAY DIFFRACTION5( CHAIN A AND RESID 142:155 )A142 - 155
6X-RAY DIFFRACTION6( CHAIN A AND RESID 156:169 )A156 - 169
7X-RAY DIFFRACTION7( CHAIN A AND RESID 170:177 )A170 - 177
8X-RAY DIFFRACTION8( CHAIN A AND RESID 178:186 )A178 - 186
9X-RAY DIFFRACTION9( CHAIN A AND RESID 187:194 )A187 - 194
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
11X-RAY DIFFRACTION10( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
12X-RAY DIFFRACTION11( CHAIN C AND RESID 1:6 )C1 - 6

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