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

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Basic information

Entry
Database: PDB / ID: 6dpi
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 40 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


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: 1.347 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 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)20,89319
Polymers19,9274
Non-polymers96615
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-84 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.620, 37.290, 62.382
Angle α, β, γ (deg.)90.00, 96.98, 90.00
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: 16272.360 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, 218 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Rb
#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.: 4 / 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.: 203 / 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: 49.46 % / 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 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→19.98 Å / Num. obs: 40007 / % possible obs: 96.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.35-1.370.77317340.3750.7731.09381.7
7.25-19.980.0162660.9990.0160.02392.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1ZBL

1zbl


Resolution: 1.347→19.981 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 1953 4.88 %
Rwork0.1451 --
obs0.1465 39993 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.347→19.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 243 44 203 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071466
X-RAY DIFFRACTIONf_angle_d1.0332022
X-RAY DIFFRACTIONf_dihedral_angle_d22.262571
X-RAY DIFFRACTIONf_chiral_restr0.072221
X-RAY DIFFRACTIONf_plane_restr0.006212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.347-1.38070.29941320.29912365X-RAY DIFFRACTION85
1.3807-1.4180.25491240.26932697X-RAY DIFFRACTION95
1.418-1.45970.24471430.24682658X-RAY DIFFRACTION96
1.4597-1.50680.24021250.21632711X-RAY DIFFRACTION96
1.5068-1.56060.2151140.18552717X-RAY DIFFRACTION96
1.5606-1.62310.2111290.17362730X-RAY DIFFRACTION97
1.6231-1.69690.17511670.15392711X-RAY DIFFRACTION97
1.6969-1.78630.17551300.14712737X-RAY DIFFRACTION97
1.7863-1.89820.16831480.14932701X-RAY DIFFRACTION98
1.8982-2.04460.18191440.14252778X-RAY DIFFRACTION98
2.0446-2.25010.16851570.13422758X-RAY DIFFRACTION98
2.2501-2.57510.15471420.13812779X-RAY DIFFRACTION99
2.5751-3.24220.18271570.13922799X-RAY DIFFRACTION99
3.2422-19.9830.1451410.11682899X-RAY DIFFRACTION99
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)
16.59561.86771.54043.7118-1.26235.8678-0.06290.3646-0.0011-0.3263-0.0994-0.90320.09741.36640.24710.18590.07340.06350.4375-0.00130.320940.485-4.322618.9277
28.6103-2.14277.35372.1743-2.1478.49740.30510.1101-0.4644-0.1621-0.07410.09630.3333-0.0503-0.29650.1260.00690.00590.0869-0.00590.154519.7343-6.043416.9312
36.6235-3.4406-5.74697.76140.58148.7119-0.126-0.4587-1.34280.13130.0023-0.34680.70670.30970.11230.19860.0244-0.01790.15390.05060.288527.6254-11.548824.0727
46.9224-0.7298-0.29177.7557-5.88176.96930.0887-0.4917-0.4883-0.02570.35910.61570.1897-0.8661-0.45830.1311-0.0434-0.00760.2525-0.00490.194110.0945-4.793318.5924
54.1992-1.09982.44751.1566-0.09754.3240.0204-0.12980.0434-0.0359-0.0210.0057-0.1484-0.0719-0.01250.08950.00210.03140.0755-0.00250.126424.43712.228522.6642
67.4634-2.02961.28111.8819-1.98454.25970.1356-0.02030.4167-0.181-0.20310.4118-0.3427-0.68270.02920.20960.13210.01050.2653-0.05860.19698.57297.921816.0715
77.46062.4356.78192.66752.85967.16390.1174-0.46660.06590.034-0.20440.1222-0.1897-0.67620.09120.13540.05510.02220.2204-0.02920.163212.32215.821224.9293
83.395-4.4792-5.20747.56395.7748.79510.0345-0.6740.6224-0.05430.3435-0.3536-0.38490.4082-0.24060.1462-0.0005-0.00070.1773-0.02460.185626.84878.353430.5448
92.12930.3020.1327.78535.20128.56910.24830.65570.0423-0.593-0.1651-0.5907-0.06150.4346-0.19270.15750.06010.07010.29830.03550.1834.3278-1.033412.3092
108.53713.0753-6.22112.4039-0.46117.9306-0.18350.8647-0.7404-0.5503-0.00470.24340.6155-0.21310.24870.30770.0646-0.03160.226-0.08180.238825.2118-9.696212.5224
114.63851.07592.87976.5191-0.16083.3552-0.04630.39710.034-0.6731-0.2236-0.32130.01670.35370.26320.21520.07430.05570.18570.00690.143823.70961.32554.5826
123.6421-0.4726-1.66014.12092.8397.23930.05440.3305-0.1113-0.7439-0.340.1786-0.3341-0.32460.29340.25390.0807-0.02410.14020.00380.128916.41063.83143.164
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 )B1 - 4
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:6 )C1 - 6

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