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- PDB-6dpo: Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in... -

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Basic information

Entry
Database: PDB / ID: 6dpo
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 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


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 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_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)21,19320
Polymers19,9274
Non-polymers1,26616
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-42 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.296, 38.002, 61.869
Angle α, β, γ (deg.)90.000, 96.060, 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: 16272.427 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Mutation: E188A
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, 187 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.49 Å3/Da / Density % sol: 50.63 % / 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: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→19.83 Å / Num. obs: 33161 / % possible obs: 98 % / Redundancy: 1 % / Biso Wilson estimate: 21.39 Å2 / Net I/σ(I): 9.5 / Num. measured all: 33161
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.45-1.4711440187.1
7.92-19.831198187.1

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Processing

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

1zbl


Resolution: 1.45→19.83 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.64
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1864 3183 4.94 %
Rwork0.1588 --
obs0.1603 64494 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.82 Å2 / Biso mean: 33.471 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 1.45→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 244 50 171 1550
Biso mean--60.42 42.43 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081484
X-RAY DIFFRACTIONf_angle_d1.0742050
X-RAY DIFFRACTIONf_chiral_restr0.068225
X-RAY DIFFRACTIONf_plane_restr0.007208
X-RAY DIFFRACTIONf_dihedral_angle_d22.433578
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 (%)
1.4457-1.46720.38971250.30872285241085
1.4672-1.49010.30421320.30972752288498
1.4901-1.51460.31321430.29562622276597
1.5146-1.54070.32921260.29212669279598
1.5407-1.56870.26961530.24982670282399
1.5687-1.59880.26951350.22742713284898
1.5988-1.63150.25851570.20562664282199
1.6315-1.66690.19631420.20232696283898
1.6669-1.70570.24111310.19152657278899
1.7057-1.74830.2071210.17712675279698
1.7483-1.79550.23581360.17662750288699
1.7955-1.84830.19971450.18212639278498
1.8483-1.9080.24741540.20212668282298
1.908-1.97610.24681490.19982681283099
1.9761-2.05510.17071100.15182746285699
2.0551-2.14860.17931660.15932675284199
2.1486-2.26170.25311300.16542700283099
2.2617-2.40320.19691420.15432693283599
2.4032-2.58830.2051210.15552733285499
2.5883-2.84810.19761350.14972671280699
2.8481-3.25870.1851310.14442698282999
3.2587-4.09960.14541510.12632682283398
4.0996-19.83380.13421480.13362572272096
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)
13.1503-2.16080.45713.0232-1.21457.58830.39660.92770.0563-0.3701-0.5407-0.6533-0.54741.4883-0.07920.23430.0960.05210.52670.02730.356640.61-3.75719.028
22.18020.67941.75991.7441.69622.42720.44010.0229-0.3326-0.0814-0.27490.00230.4136-0.0275-0.28190.23410.00710.00110.18850.02190.21522.79-5.8816.767
36.0716-1.89035.31251.1934-1.78274.37060.40240.324-0.4681-0.1551-0.19390.07980.41220.1615-0.32660.2221-0.0041-0.02230.2075-0.01230.244617.859-6.35216.478
47.1096-2.5309-5.10965.65560.44767.1361-0.0376-0.376-1.2039-0.0104-0.0429-0.52140.9240.37620.04110.24680.0552-0.01310.14060.0440.352627.441-11.52223.759
57.8322-4.21544.62394.9476-5.04455.19680.1204-0.6205-0.6062-0.18270.52470.81120.2411-1.2867-0.61430.2279-0.0228-0.01560.3189-0.00550.251110.537-5.08518.561
65.4096-0.86814.89791.39750.24486.78030.0296-0.3338-0.0686-0.027-0.01390.0607-0.1251-0.344-0.03590.12690.00840.03490.1410.0050.18421.2040.65323.883
72.6317-0.88562.44781.7694-0.00442.73220.1087-0.0748-0.0673-0.0098-0.054-0.09930.11730.0353-0.05430.1548-0.00710.0160.21820.02120.208631.048-0.84225.32
86.3644-6.5399-1.56429.08331.71637.77210.16650.11810.4511-0.1745-0.1274-0.4671-0.96120.27620.00410.2765-0.020.0190.13530.04620.230724.0238.80616.089
97.86062.59362.62923.49940.18073.62960.5067-0.04270.6813-0.0585-0.64340.4916-0.9331-1.14660.10450.33370.2965-0.01520.498-0.13330.299.67.88516.375
109.42331.18886.2231.90712.67649.02310.128-0.3116-0.00940.0023-0.31410.1745-0.2371-0.86630.26330.18870.07810.01890.2513-0.04830.207213.1976.47525.551
116.319-6.7166-5.38637.09165.73484.61470.0554-0.57650.3267-0.12420.1676-0.3607-0.10410.4531-0.25220.18230.00150.00980.2394-0.0170.242628.4347.52829.904
123.2954-0.844-0.27576.88795.18234.07340.35530.7545-0.1078-0.6133-0.2351-0.6505-0.00640.3322-0.26170.28130.10850.07990.38510.03830.233434.724-0.67712.262
138.6373-2.505-7.79523.18471.85767.19690.09330.4358-0.6765-0.1935-0.08390.07770.70460.04110.00620.31360.1-0.02190.2551-0.07770.255727.961-9.16213.858
147.40971.41532.45197.83290.1853.80480.06860.2884-0.3076-0.7795-0.238-0.2650.20770.34750.15120.3390.09020.03650.23490.00110.153222.681-0.184.762
153.2498-1.5139-0.7264.06993.12948.46150.06980.2817-0.154-1.0003-0.44540.1624-0.5511-0.32250.40510.43880.0948-0.02750.22990.00260.183316.3933.5423.149
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 67:75 )A67 - 75
3X-RAY DIFFRACTION3( CHAIN A AND RESID 76:87 )A76 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:96 )A88 - 96
5X-RAY DIFFRACTION5( CHAIN A AND RESID 97:104 )A97 - 104
6X-RAY DIFFRACTION6( CHAIN A AND RESID 105:122 )A105 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:133 )A123 - 133
8X-RAY DIFFRACTION8( CHAIN A AND RESID 134:141 )A134 - 141
9X-RAY DIFFRACTION9( CHAIN A AND RESID 142:155 )A142 - 155
10X-RAY DIFFRACTION10( CHAIN A AND RESID 156:171 )A156 - 171
11X-RAY DIFFRACTION11( CHAIN A AND RESID 172:177 )A172 - 177
12X-RAY DIFFRACTION12( CHAIN A AND RESID 178:186 )A178 - 186
13X-RAY DIFFRACTION13( CHAIN A AND RESID 187:193 )A187 - 193
14X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
15X-RAY DIFFRACTION14( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
16X-RAY DIFFRACTION15( CHAIN C AND RESID 1:6 )C1 - 6

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