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

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Basic information

Entry
Database: PDB / ID: 6dpl
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 720 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


DNA replication, removal of RNA primer / 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 / Ribonuclease H1 N-terminal domain / : / 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, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / 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
RUBIDIUM ION / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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_asym_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)21,45826
Polymers19,9274
Non-polymers1,53122
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-112 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.856, 37.521, 62.706
Angle α, β, γ (deg.)90.000, 97.310, 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, 191 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.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / 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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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: 50.14 % / 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: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→19.5 Å / Num. obs: 33423 / % possible obs: 98.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 17.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.03 / Rrim(I) all: 0.043 / Net I/σ(I): 13.1 / Num. measured all: 64252
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.470.77814290.3710.7781.188.5
7.94-19.50.0162160.9990.0160.02393.3

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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: 1.45→19.495 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 19.91
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1792 3183 4.9 %
Rwork0.1506 --
obs0.152 65009 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.89 Å2 / Biso mean: 28.869 Å2 / Biso min: 11.74 Å2
Refinement stepCycle: final / Resolution: 1.45→19.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 244 67 169 1586
Biso mean--64.64 42.13 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071520
X-RAY DIFFRACTIONf_angle_d1.0242096
X-RAY DIFFRACTIONf_chiral_restr0.07228
X-RAY DIFFRACTIONf_plane_restr0.006216
X-RAY DIFFRACTIONf_dihedral_angle_d23.007598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4488-1.47040.27691300.30072271240188
1.4704-1.49340.33241440.29892631277594
1.4934-1.51790.29841520.28632541269395
1.5179-1.54410.35321270.2822687281498
1.5441-1.57210.31831120.257127172829100
1.5721-1.60230.24991430.248127162859100
1.6023-1.6350.26261460.230227412887100
1.635-1.67060.24031040.21727622866100
1.6706-1.70940.18021580.204826772835100
1.7094-1.75210.24121410.179326922833100
1.7521-1.79950.17071260.184527952921100
1.7995-1.85240.20941460.179226762822100
1.8524-1.91210.20651460.168427082854100
1.9121-1.98040.19841360.158227632899100
1.9804-2.05960.19291460.141427012847100
2.0596-2.15320.17041700.138126932863100
2.1532-2.26660.16251220.136427392861100
2.2666-2.40840.19081330.139927152848100
2.4084-2.59390.17951470.142626992846100
2.5939-2.85420.18021210.143227622883100
2.8542-3.26560.16751610.135826832844100
3.2656-4.10790.13061270.109327542881100
4.1079-19.49710.13691450.121327032848100
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)
15.37320.20562.40173.8118-0.39526.24270.0350.59730.0359-0.4988-0.2431-0.8610.10051.40640.15090.17850.09530.06720.4790.02290.324340.102-4.6618.995
25.093-2.90356.10652.68-3.1077.51170.40130.1055-0.4643-0.2014-0.13220.13290.5026-0.028-0.28240.13460.00850.01230.1485-0.00730.166119.562-6.02517.126
37.4385-4.3728-6.02797.75632.12418.853-0.101-0.4244-1.51750.1141-0.0057-0.34270.83280.27680.16430.18980.04940.00430.19390.07470.351327.4-11.53224.314
45.5215-3.90693.6644.9914-5.07345.43010.0709-0.6922-0.5297-0.06820.41260.75360.2973-1.163-0.52780.1808-0.0374-0.00030.31120.00290.20729.877-4.76718.783
54.183-1.31172.69581.7091-0.37965.23580.0386-0.12920.0079-0.025-0.0215-0.0108-0.1275-0.1025-0.02650.077-0.00290.03450.09750.00260.125324.2332.16523.201
67.0775-1.770621.3816-1.94146.0360.06590.1680.657-0.2129-0.13980.5368-0.1846-0.55230.04840.20780.14330.02430.2509-0.0550.22658.2497.89316.189
78.15222.86877.19272.01623.01556.86-0.0367-0.56090.17560.0711-0.20430.1379-0.1552-0.62420.28020.14660.05230.0220.2213-0.03810.179212.8626.61525.799
85.6141-3.6138-4.32966.7895.7287.970.23940.07840.2585-0.2709-0.0146-0.4162-0.17120.3776-0.32010.09690.00220.03040.18470.05090.182831.6842.51319.922
98.14390.0295-4.92064.9923-1.60247.42140.07430.8132-0.6912-0.7229-0.05010.0930.91260.1252-0.03190.31920.0799-0.0210.2066-0.08050.210825.331-9.70512.669
106.33013.26180.90055.7532-0.97260.9777-0.00260.1584-0.1332-0.469-0.2134-0.23550.07850.12160.24330.24250.08540.04450.22190.00330.155923.7080.6965.093
112.5588-0.5602-1.31343.94635.27037.4836-0.01250.2633-0.0888-0.999-0.36350.1276-0.6071-0.43420.40540.3380.0658-0.02270.19330.0160.159216.3493.6113.286
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 156:171 )A156 - 171
8X-RAY DIFFRACTION8( CHAIN A AND RESID 172:186 )A172 - 186
9X-RAY DIFFRACTION9( CHAIN A AND RESID 187:196 )A187 - 196
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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