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- PDB-6dp8: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6dp8
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Li+ for 240 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 / 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
: / DI(HYDROXYETHYL)ETHER / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.323 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 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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
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_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_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_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.pdbx_dist_value / _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

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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)21,00821
Polymers19,9854
Non-polymers1,02317
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-57 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.426, 37.747, 61.811
Angle α, β, γ (deg.)90.000, 95.450, 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 construct (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 construct (others)

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 16330.462 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (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 , 7 types, 225 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-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li / 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.44 Å3/Da / Density % sol: 49.49 % / 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 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→23.46 Å / Num. obs: 41833 / % possible obs: 95.6 % / Redundancy: 1 % / Biso Wilson estimate: 16.78 Å2 / Net I/σ(I): 8.6 / Num. measured all: 41833
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.32-1.3511760182
7.24-23.461280195.9

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Processing

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

1zbl


Resolution: 1.323→23.455 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.72
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1702 4068 4.97 %
Rwork0.1468 --
obs0.1479 81810 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110 Å2 / Biso mean: 24.9905 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.323→23.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 62 208 1624
Biso mean--54.48 38.48 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081496
X-RAY DIFFRACTIONf_angle_d1.0562047
X-RAY DIFFRACTIONf_chiral_restr0.071221
X-RAY DIFFRACTIONf_plane_restr0.007214
X-RAY DIFFRACTIONf_dihedral_angle_d25.394587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3229-1.33850.36531240.32912252237680
1.3385-1.35480.3461160.31412586270291
1.3548-1.37190.35391520.2852602275493
1.3719-1.390.2441220.28352631275394
1.39-1.4090.29011240.26182625274994
1.409-1.42920.28221470.25122628277595
1.4292-1.45050.25961420.23692749289195
1.4505-1.47310.26511460.2192554270094
1.4731-1.49730.26321430.20862716285995
1.4973-1.52310.19971530.20482611276495
1.5231-1.55080.23391440.18752674281895
1.5508-1.58060.19351370.17772656279396
1.5806-1.61290.22041460.16452682282896
1.6129-1.64790.21481510.16022693284496
1.6479-1.68630.18251470.15072660280796
1.6863-1.72840.15931350.13822751288696
1.7284-1.77510.15541360.13562683281996
1.7751-1.82740.16981570.14032643280097
1.8274-1.88630.19481340.14772781291597
1.8863-1.95370.17491770.13982700287797
1.9537-2.03190.14871450.13112718286397
2.0319-2.12430.13051360.12822721285798
2.1243-2.23620.14591400.12752767290798
2.2362-2.37620.1741540.13432746290098
2.3762-2.55950.15581360.14012745288198
2.5595-2.81660.16491430.14292787293099
2.8166-3.22330.15431290.13942778290799
3.2233-4.05760.15151370.11962801293899
4.0576-23.45890.13281150.13442802291799
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)
13.36331.4583-3.00198.6429-0.69213.43920.15590.75850.5098-0.5628-0.1863-1.0167-0.05231.12720.02130.17690.07090.03330.41350.02720.37241.1107-3.531419.1328
24.4704-1.81325.81640.9431-2.24667.62380.3282-0.0284-0.3338-0.136-0.07310.06670.4247-0.1891-0.23030.1331-0.00360.0030.1083-0.01960.151420.0259-6.334216.1651
33.0564-0.32461.43081.0602-0.45013.22120.038-0.0925-0.0688-0.0342-0.04550.00170.0708-0.04670.0070.0820.00640.03370.084-0.00340.119423.5261-1.298422.2618
46.38092.11262.69954.28360.90254.8020.12470.03770.3794-0.0538-0.28730.4568-0.1088-0.61580.10960.1830.10010.01630.2553-0.07170.22539.75927.543116.6908
53.8035-1.41360.11722.40591.06013.9008-0.0121-0.39970.26280.0756-0.11910.0557-0.1341-0.35170.13130.11780.0120.02840.1206-0.01220.121718.12486.507127.096
63.3626-1.7794-1.77665.53094.34583.74080.18250.49360.1479-0.65940.0503-0.6569-0.29330.7159-0.29890.18770.05070.08330.32150.03510.206635.2727-0.129312.3398
71.07730.7224-1.04952.4071-0.54461.4975-0.01551.0018-0.4272-0.57180.0452-0.16710.62380.0781-0.05240.29170.0630.01620.2687-0.06460.211327.1422-9.701311.543
82.02831.27841.4186.1888-0.02852.2613-0.00790.24610.0562-0.3825-0.1333-0.07680.11150.19450.14590.18850.04870.03360.22390.01120.164124.01351.55234.6657
94.20971.03950.71797.85725.25256.8255-0.07470.3689-0.0827-0.8077-0.156-0.0113-0.38520.08580.25350.21390.05670.00670.14710.02260.12716.67493.8253.2345
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 141 )A88 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 155 )A142 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 177 )A156 - 177
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 186 )A178 - 186
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 195 )A187 - 195
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 6 )B1 - 6
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 6 )C1 - 6

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