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- PDB-6dp9: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6dp9
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 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 / 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 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: 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)20,59819
Polymers19,3714
Non-polymers1,22715
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-28 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.091, 37.976, 61.408
Angle α, β, γ (deg.)90.000, 95.960, 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 (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 (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
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 (others)

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Non-polymers , 6 types, 196 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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, and the LINK record was ...Note that chain B was split into 2 chains (B and b) at the position 4-5, and the LINK record was introduced to link these two chains. This was done to accommodate the cases observed in the related entries, 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: 49.96 % / 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: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.77 Å / Num. obs: 33786 / % possible obs: 91.5 % / Redundancy: 1 % / Biso Wilson estimate: 19.03 Å2 / Net I/σ(I): 8.6 / Num. measured all: 33786
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1 % / Num. unique obs: 1478 / % possible all: 82.9

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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: 1ZBL

1zbl


Resolution: 1.4→19.767 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.13
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1843 1651 4.96 %
Rwork0.1522 --
obs0.1538 33782 91.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.36 Å2 / Biso mean: 30.3883 Å2 / Biso min: 12.98 Å2
Refinement stepCycle: final / Resolution: 1.4→19.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 243 41 181 1554
Biso mean--58.72 43.62 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081462
X-RAY DIFFRACTIONf_angle_d1.0182017
X-RAY DIFFRACTIONf_chiral_restr0.069220
X-RAY DIFFRACTIONf_plane_restr0.007211
X-RAY DIFFRACTIONf_dihedral_angle_d23.231575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3988-1.43990.38751240.29662460258486
1.4399-1.48640.27651270.26572639276691
1.4864-1.53950.25251290.23462606273589
1.5395-1.60110.24631540.20592582273689
1.6011-1.67390.22911300.18892618274890
1.6739-1.76210.24331320.17262659279191
1.7621-1.87240.18211420.16742666280891
1.8724-2.01690.17821620.14982701286393
2.0169-2.21960.18671380.14252785292395
2.2196-2.54020.17381470.1472805295296
2.5402-3.19820.18411360.15512820295695
3.1982-19.76940.1591530.12472767292092
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)
18.11770.9099-4.87186.9260.28898.11380.09530.9826-0.0346-0.4782-0.6314-1.08120.17171.37950.45060.24930.10880.04780.44720.04260.346240.9458-3.920618.6134
21.99512.22762.22672.65292.64322.66340.2481-0.1505-0.0641-0.0559-0.22860.1290.3606-0.2742-0.08530.2201-0.02310.0060.2470.02620.171121.8827-6.396715.7768
38.39460.48667.84680.2241-0.09998.80360.35240.2501-0.4951-0.249-0.18960.09230.1475-0.1038-0.17530.2172-0.015-0.0020.1643-0.02430.169118.2114-6.650616.4096
47.3903-1.7566-6.37696.35310.87997.7817-0.3399-0.6706-1.43240.07110.0724-0.58050.66780.60440.1590.2410.05540.01720.18190.03570.342128.3409-11.502423.6796
58.5463-4.48134.45329.5241-8.09289.14550.0197-0.5028-0.4976-0.08310.43320.54990.2072-0.9843-0.47290.1801-0.0117-0.00430.2402-0.03430.158910.6078-5.173818.368
65.8135-0.87493.67510.714-0.10684.62240.004-0.1970.0048-0.0644-0.0209-0.03240.0316-0.13770.00530.1417-0.00150.02480.07140.00970.121824.8960.078824.2365
75.2691-3.0949-1.42015.5133-1.46067.12870.21350.07970.4835-0.0867-0.0761-0.3789-0.9009-0.0205-0.11490.287-0.01510.05580.13590.03120.189523.91649.643316.2273
83.35771.76652.05221.7327-0.22273.39170.1415-0.04930.798-0.2036-0.53430.4603-1.0427-0.51130.05360.39850.2489-0.00130.3904-0.10610.2711.02359.24915.906
99.14561.02624.46664.81490.45445.20780.20590.0076-0.1252-0.1213-0.25110.4593-0.0698-0.71710.03110.17140.06270.02580.2829-0.06160.17110.36554.84323.1217
106.9072-5.1904-7.03276.95546.53588.73990.2535-0.45830.5439-0.26830.1538-0.3157-0.3480.272-0.34110.1888-0.00150.01170.15210.00910.152826.45528.498729.9894
114.27692.1957-0.40856.40923.82169.55740.02490.7688-0.1833-0.7557-0.0703-0.60060.2160.6452-0.07510.29650.07280.09660.34070.0290.199734.712-0.547112.0276
125.1753-1.3109-3.06763.45011.97466.726-0.31481.2336-0.9522-0.87880.1223-0.3930.8816-0.45560.1290.51580.01130.05250.4008-0.090.23927.3398-9.37212.6752
134.3277-0.72222.84395.71880.0572.17830.00380.63550.0057-0.6547-0.1274-0.32230.06240.23830.12990.36040.05280.05770.26650.00630.147923.80481.34884.3174
142.6724-1.9997-3.40741.88321.25177.64770.10420.4135-0.0871-0.8574-0.49440.1496-0.4651-0.33850.37030.44720.0999-0.01490.23480.0090.167116.3553.62452.9938
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 105:133 )A105 - 133
7X-RAY DIFFRACTION7( CHAIN A AND RESID 134:142 )A134 - 142
8X-RAY DIFFRACTION8( CHAIN A AND RESID 143:152 )A143 - 152
9X-RAY DIFFRACTION9( CHAIN A AND RESID 153:169 )A153 - 169
10X-RAY DIFFRACTION10( CHAIN A AND RESID 170:177 )A170 - 177
11X-RAY DIFFRACTION11( CHAIN A AND RESID 178:186 )A178 - 186
12X-RAY DIFFRACTION12( CHAIN A AND RESID 187:194 )A187 - 194
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
14X-RAY DIFFRACTION13( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
15X-RAY DIFFRACTION14( CHAIN C AND RESID 1:6 )C1 - 6

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