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

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Basic information

Entry
Database: PDB / ID: 6dot
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 40 s at 21 C
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of uncleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • 5'-R(P*CP*G)-3' portion of uncleaved 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 / 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
RUBIDIUM ION / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.423 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_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 uncleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
b: 5'-R(P*CP*G)-3' portion of uncleaved 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)20,30518
Polymers19,3714
Non-polymers93414
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-91 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.557, 37.229, 62.052
Angle α, β, γ (deg.)90.000, 96.610, 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 uncleaved 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 uncleaved 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: 15716.729 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
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 construct (others)

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Non-polymers , 6 types, 228 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-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 49.3 % / 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: 0.8 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: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.42→23.35 Å / Num. obs: 34770 / % possible obs: 99.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 11.8 / Num. measured all: 67551
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.42-1.451.90.42215270.5930.4220.59787.3
7.79-23.351.70.0282310.9950.0280.0496.4

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: 1ZBL

1zbl


Resolution: 1.423→23.348 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.51
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1684 1772 5.11 %
Rwork0.1424 --
obs0.1437 34770 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.44 Å2 / Biso mean: 27.9634 Å2 / Biso min: 13.26 Å2
Refinement stepCycle: final / Resolution: 1.423→23.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 243 42 214 1599
Biso mean--53.34 41.69 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071460
X-RAY DIFFRACTIONf_angle_d1.0112015
X-RAY DIFFRACTIONf_chiral_restr0.069219
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d22.232570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.423-1.44250.33281220.26352213233584
1.4425-1.46310.26051190.234125432662100
1.4631-1.4850.24181330.212126382771100
1.485-1.50820.2211080.192825942702100
1.5082-1.53290.19921300.190925832713100
1.5329-1.55930.21251470.175225452692100
1.5593-1.58770.1931790.178725812760100
1.5877-1.61820.21591380.172125742712100
1.6182-1.65120.24431120.158826182730100
1.6512-1.68710.23171350.156225722707100
1.6871-1.72630.18261630.147426222785100
1.7263-1.76950.17871370.152625182655100
1.7695-1.81730.19931410.146325982739100
1.8173-1.87080.22371420.146726222764100
1.8708-1.93110.17261230.152325122635100
1.9311-2.00010.15861310.143326192750100
2.0001-2.08010.16141400.138725692709100
2.0801-2.17480.14611190.137125912710100
2.1748-2.28930.15381780.136725442722100
2.2893-2.43260.18461250.137826132738100
2.4326-2.62020.18781460.147125642710100
2.6202-2.88350.15921550.138725832738100
2.8835-3.29970.15821000.136226102710100
3.2997-4.15350.12691310.117325802711100
4.1535-23.35070.15881970.135325392736100
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)
15.6996-1.5394-2.69738.8481-0.40983.53180.1680.52510.1647-0.619-0.4065-0.61740.10481.65350.22160.1960.0650.0330.47950.01770.286340.699-4.25418.791
26.2722-0.31486.20420.7737-0.76298.59260.24990.056-0.3823-0.1045-0.0684-0.00130.3313-0.066-0.24840.1870.0116-0.00250.1162-0.0020.197219.339-6.25616.302
35.9512-0.6385-6.62342.00110.58997.4062-0.1496-0.4478-1.26770.0263-0.0356-0.31780.63750.46620.19240.23840.0408-0.00440.19250.04430.341527.922-11.57823.848
46.1481-1.9732.30188.8357-6.74437.80130.0955-0.3794-0.4509-0.13310.24070.49750.2939-0.9129-0.37810.1543-0.03090.00140.235-0.01360.174510.343-4.82818.478
53.9018-1.29642.76881.2205-0.13954.69250.0203-0.05490.0745-0.0673-0.044-0.0068-0.1634-0.0379-0.00520.1275-0.00110.02260.09220.00330.149724.6232.22222.564
66.4495-0.9573.48231.3864-1.52765.55540.0859-0.28630.4297-0.1656-0.25650.4414-0.3799-0.73580.12870.29030.16420.00960.2736-0.06520.22488.7747.87315.97
77.28642.30986.96354.1851.70858.39570.1732-0.33060.0580.01-0.25090.1027-0.1033-0.55610.10940.16720.04990.02360.2193-0.03260.178112.4915.78224.814
84.8644-5.4649-5.8458.23326.09527.21960.225-0.4550.7275-0.18820.2952-0.4602-0.40670.3379-0.36450.1725-0.0040.00320.1814-0.01770.189526.9958.35230.431
94.1918-0.92590.60794.95033.85144.49530.44960.7358-0.1266-0.7257-0.2979-0.5764-0.05560.3969-0.19220.21750.0580.06780.28720.03880.193134.535-0.91312.212
104.52322.6715-5.78057.2684-0.84948.5384-0.08990.8777-0.5814-0.5243-0.09130.15160.4869-0.33350.14710.31140.0525-0.03020.2545-0.07120.228925.523-9.72212.446
116.46340.02553.56354.32420.33474.0605-0.01880.615-0.1558-0.5321-0.1491-0.36990.03620.31480.17860.2740.06810.05250.22420.00230.171723.8631.3614.495
124.9957-0.4611-1.4983.93832.16227.7342-0.0120.4228-0.1569-0.811-0.27880.1948-0.2541-0.27380.27140.34410.08-0.0230.18330.01170.157416.4783.8013.142
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 105:142 )A105 - 142
6X-RAY DIFFRACTION6( CHAIN A AND RESID 143:155 )A143 - 155
7X-RAY DIFFRACTION7( CHAIN A AND RESID 156:169 )A156 - 169
8X-RAY DIFFRACTION8( CHAIN A AND RESID 170:177 )A170 - 177
9X-RAY DIFFRACTION9( CHAIN A AND RESID 178:186 )A178 - 186
10X-RAY DIFFRACTION10( CHAIN A AND RESID 187:195 )A187 - 195
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
12X-RAY DIFFRACTION11( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
13X-RAY DIFFRACTION12( CHAIN C AND RESID 1:6 )C1 - 6

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