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

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Basic information

Entry
Database: PDB / ID: 6dpp
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 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 / 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
RUBIDIUM ION / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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)20,54022
Polymers19,3714
Non-polymers1,16918
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-108 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.468, 37.992, 62.477
Angle α, β, γ (deg.)90.000, 96.810, 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: 15716.729 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
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 , 6 types, 198 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.: 5 / 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.: 3 / 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.: 180 / 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: 50.25 % / 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: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→19.94 Å / Num. obs: 33303 / % possible obs: 98.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.026 / Rrim(I) all: 0.037 / Net I/σ(I): 14.3 / Num. measured all: 63571
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.471.70.649208712550.4720.6490.918177.3
7.94-19.941.80.0183752120.9980.0180.02648.792.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: pdbid 1ZBL

1zbl


Resolution: 1.45→19.936 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.27
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1707 1689 4.96 %
Rwork0.1513 --
obs0.1523 64738 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.03 Å2 / Biso mean: 29.2129 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 1.45→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 48 180 1582
Biso mean--53.54 41.54 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081493
X-RAY DIFFRACTIONf_angle_d1.0192041
X-RAY DIFFRACTIONf_chiral_restr0.069225
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d22.171585
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 (%)
1.4498-1.47140.3731200.30962003212376
1.4714-1.49440.29881350.29682534266990
1.4944-1.51890.29361410.2722555269694
1.5189-1.54510.28841200.2552646276698
1.5451-1.57320.27651560.23772667282399
1.5732-1.60340.21871360.226227502886100
1.6034-1.63610.25251420.208327242866100
1.6361-1.67170.19041650.196527292894100
1.6717-1.71060.23781230.181427372860100
1.7106-1.75330.19151240.174227112835100
1.7533-1.80070.2181450.16627562901100
1.8007-1.85360.17481390.172327132852100
1.8536-1.91340.17441570.154227192876100
1.9134-1.98180.21191460.157227212867100
1.9818-2.0610.18021130.143727632876100
2.061-2.15470.16011690.139127062875100
2.1547-2.26820.19011250.139227322857100
2.2682-2.41010.14821440.139827402884100
2.4101-2.59580.16581330.147827432876100
2.5958-2.85630.18261350.152127082843100
2.8563-3.26810.1581330.138227322865100
3.2681-4.11150.14141510.12427502901100
4.1115-19.93820.13421570.130126902847100
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)
12.92950.4292-2.13953.7273-1.5342.82070.06540.57330.2118-0.3913-0.5222-0.92350.15561.47480.36650.22140.08840.0490.50890.04980.313440.4779-4.389418.9757
26.9434-1.325.03751.6545-1.34714.08470.35990.1486-0.4207-0.1734-0.12240.12820.4141-0.0637-0.30940.18460.0086-0.00730.1521-0.00590.177819.0631-6.307916.629
39.8061-3.9963-6.18018.80661.61344.0204-0.2648-0.4208-1.36690.24290.0668-0.41540.64440.29560.21770.22920.0507-0.02360.19470.05550.306827.6046-11.599824.2149
44.8847-0.04412.40151.04110.23814.46560.1104-0.2939-0.1506-0.0041-0.05970.06390.0674-0.3234-0.03910.11390.01270.01670.07960.01180.129321.6915-0.91623.488
55.4587-3.83360.40845.83812.03532.95820.12180.11020.6483-0.2875-0.1603-0.4189-1.00050.25930.06580.2812-0.00890.02510.13480.05560.2123.72929.407516.6665
68.0319-0.56472.35032.1475-2.35915.24520.19550.03230.6666-0.1778-0.20330.5979-0.3775-0.81330.00250.29660.17870.00240.3393-0.07770.25488.38827.909916.115
75.03764.67816.90526.37045.80259.82730.1457-0.40720.17770.0092-0.29410.2324-0.1068-0.61210.1740.16050.05970.01430.22-0.02930.183312.25075.913824.9618
85.5321-5.7429-1.23989.15314.94984.46420.0715-0.66370.7204-0.10340.3018-0.4377-0.26240.3492-0.29070.1844-0.0099-0.00210.1816-0.00650.180326.28498.462330.4142
94.5575-1.30560.53458.68255.4534.13660.33160.5733-0.0238-0.5707-0.1712-0.5378-0.05160.3879-0.22360.20790.06230.0610.26770.03880.187234.2538-1.020412.4489
102.94193.4493-3.08198.00790.61918.34-0.02120.5957-0.5099-0.45940.13610.29190.6255-0.0683-0.0890.29190.0622-0.03150.2031-0.0540.218224.7576-9.861211.9015
112.8091-0.19332.28748.9711-2.17862.5250.08720.1301-0.0705-0.766-0.4154-0.45240.07110.20630.34110.28390.08720.04920.23430.01290.146323.53120.68585.2143
122.5502-0.3331-1.68917.3335.26494.8766-0.09090.1693-0.0086-1.0916-0.31640.2366-0.6327-0.38240.43610.40090.0758-0.04120.21860.02350.16416.32153.46863.2836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )A61 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 87 )A67 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 96 )A88 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 133 )A97 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 142 )A134 - 142
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )A143 - 155
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 169 )A156 - 169
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 177 )A170 - 177
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 186 )A178 - 186
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 196 )A187 - 196
11X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4 )) OR (chain 'b' and (resid 5 through 6 ))B1 - 4
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )C1 - 6
13X-RAY DIFFRACTION11(chain 'B' and (resid 1 through 4 )) OR (chain 'b' and (resid 5 through 6 ))b5 - 6

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