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- PDB-6dp7: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6dp7
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 500 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')
  • RNA (5'-R(P*CP*G)-3')
  • 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 / 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 / : / : / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.381 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
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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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')
b: RNA (5'-R(P*CP*G)-3')
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,00614
Polymers19,2424
Non-polymers76410
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-37 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.013, 37.557, 61.932
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 RNA (5'-R(*AP*CP*AP*U)-3')


Mass: 1224.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*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: 15587.549 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 construct (others)

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Non-polymers , 5 types, 179 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsNote that chain B was split into 2 chains (B and b) at the position 4-5, where the cleavage does occur

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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: 2.46 Å3/Da / Density % sol: 49.9 % / 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: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→17.98 Å / Num. obs: 38088 / % possible obs: 98.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Net I/σ(I): 10.1 / Num. measured all: 74048
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.296 / Num. measured all: 2990 / Num. unique obs: 1523 / CC1/2: 0.763 / Rpim(I) all: 0.296 / Rrim(I) all: 0.419 / Net I/σ(I) obs: 4.1 / % possible all: 76.4

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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: 1.381→17.983 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 1908 5.04 %
Rwork0.1686 35979 -
obs0.1698 37887 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.9 Å2 / Biso mean: 29.3649 Å2 / Biso min: 12.39 Å2
Refinement stepCycle: final / Resolution: 1.381→17.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 244 16 169 1529
Biso mean--58.98 39.56 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071426
X-RAY DIFFRACTIONf_angle_d0.9461969
X-RAY DIFFRACTIONf_chiral_restr0.073217
X-RAY DIFFRACTIONf_plane_restr0.006207
X-RAY DIFFRACTIONf_dihedral_angle_d23.788549
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 (%)
1.3807-1.41520.30051280.24652161228983
1.4152-1.45350.27351410.24812599274099
1.4535-1.49620.29411210.23852571269299
1.4962-1.54450.22521480.23672559270798
1.5445-1.59960.20291240.194226012725100
1.5996-1.66360.21351180.179426302748100
1.6636-1.73930.20211450.177826262771100
1.7393-1.83090.22161410.177226012742100
1.8309-1.94550.26261250.22312570269598
1.9455-2.09550.1971420.176226122754100
2.0955-2.3060.18551350.176426332768100
2.306-2.63880.16431540.158526252779100
2.6388-3.32120.16361420.157126522794100
3.3212-17.98410.18171440.13972539268394
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)
13.8197-0.03771.57548.765-2.86292.74360.08810.33560.1769-0.82940.0056-1.46330.00321.98490.26720.23790.05140.06850.5174-0.05050.310640.675-4.27318.623
24.8076-2.25464.81382.1723-2.06844.93540.32830.1314-0.4796-0.2138-0.04090.12120.3599-0.1526-0.33520.2010.00180.01090.1888-0.01080.141119.716-6.12116.521
32.0024-0.7884-0.21772.01872.03342.5550.1012-0.2136-1.7450.1007-0.1155-0.41780.58990.40320.1150.24380.06880.02810.27060.030.328327.981-11.66523.753
45.4480.01963.40912.22440.36634.96270.0426-0.3392-0.1429-0.0264-0.09780.08970.0926-0.58480.03260.10570.00630.03880.1449-0.00270.08318.095-0.95822.306
54.3695-1.05732.19323.10970.90174.36590.0907-0.33-0.04280.1235-0.0145-0.22310.4138-0.083-0.04520.1154-0.00170.0330.16980.020.107731.146-1.10225.288
68.9191-6.395-2.25997.60573.67152.32340.16130.2310.7337-0.3288-0.0519-0.6413-0.70360.3228-0.15650.2562-0.00520.0540.13670.02950.147723.9599.47116.624
75.6295-0.90594.06587.84240.97048.34310.05420.07370.4592-0.3623-0.30710.7589-0.2835-0.63410.18650.22390.1621-0.00020.3078-0.09810.20358.5967.76216.126
82.78973.19391.94574.33953.53037.4550.0372-0.45680.30560.0068-0.33890.1762-0.252-0.83710.32780.18620.0648-0.00210.2415-0.0460.148813.2196.51625.533
93.74570.20180.55315.56134.95954.51130.0761-0.86591.04070.23770.3537-0.638-0.12630.8671-0.340.2259-0.0213-0.00930.25660.00650.240228.4747.32429.944
100.4038-0.9826-1.19114.13965.93348.78240.23130.59690.055-0.5343-0.122-0.4807-0.31130.3665-0.16660.22350.04780.08450.33890.02250.171834.447-0.93312.14
115.22471.0068-4.39527.15881.70514.63470.19450.6405-0.7039-0.2731-0.21940.08330.30120.05630.00720.25410.0715-0.01210.2444-0.05580.164525.529-9.75712.266
121.5058-1.8712.65255.9214-3.16155.48740.28080.09520.0397-0.5396-0.6696-0.4994-0.01140.49630.33740.30170.08350.08030.24310.03090.155723.9061.2694.468
131.2053-1.7941-2.86614.063.22727.62420.08150.16340.063-1.1326-0.55840.3238-0.8268-0.5920.39130.41660.094-0.03530.22690.00520.123416.4513.7983.062
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 97:122 )A97 - 122
5X-RAY DIFFRACTION5( CHAIN A AND RESID 123:133 )A123 - 133
6X-RAY DIFFRACTION6( CHAIN A AND RESID 134:142 )A134 - 142
7X-RAY DIFFRACTION7( CHAIN A AND RESID 143:155 )A143 - 155
8X-RAY DIFFRACTION8( CHAIN A AND RESID 156:171 )A156 - 171
9X-RAY DIFFRACTION9( CHAIN A AND RESID 172:177 )A172 - 177
10X-RAY DIFFRACTION10( CHAIN A AND RESID 178:186 )A178 - 186
11X-RAY DIFFRACTION11( CHAIN A AND RESID 187:195 )A187 - 195
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
13X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
14X-RAY DIFFRACTION13( CHAIN C AND RESID 1:6 )C1 - 6

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