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

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Basic information

Entry
Database: PDB / ID: 6dou
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 120 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 / 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 C-125 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.487 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)20,57022
Polymers19,3714
Non-polymers1,19918
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-100 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.541, 37.383, 62.437
Angle α, β, γ (deg.)90.00, 96.57, 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 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 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, 207 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.: 5 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 0.8 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: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.49→19.94 Å / Num. obs: 29596 / % possible obs: 95.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.021 / Rrim(I) all: 0.029 / Net I/σ(I): 17.8 / Num. measured all: 57072
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.49-1.510.63610190.280.6360.967.5
8.15-19.940.0131710.9990.0130.01983.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: pdbid 1ZBL

1zbl


Resolution: 1.487→19.936 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 1504 5.11 %
Rwork0.155 --
obs0.1567 29459 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.487→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 244 43 189 1593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071503
X-RAY DIFFRACTIONf_angle_d1.0342055
X-RAY DIFFRACTIONf_dihedral_angle_d21.424590
X-RAY DIFFRACTIONf_chiral_restr0.072226
X-RAY DIFFRACTIONf_plane_restr0.006213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4871-1.53510.34981000.29131963X-RAY DIFFRACTION75
1.5351-1.58990.25991240.25292412X-RAY DIFFRACTION90
1.5899-1.65350.27631540.23742548X-RAY DIFFRACTION96
1.6535-1.72870.25951520.2042564X-RAY DIFFRACTION97
1.7287-1.81980.20971430.1972564X-RAY DIFFRACTION98
1.8198-1.93380.26931430.19082589X-RAY DIFFRACTION98
1.9338-2.08290.18221620.16562609X-RAY DIFFRACTION98
2.0829-2.29230.20281230.15252636X-RAY DIFFRACTION98
2.2923-2.62330.19161300.15692667X-RAY DIFFRACTION99
2.6233-3.30270.19751300.14832677X-RAY DIFFRACTION99
3.3027-19.93780.14341430.1262726X-RAY DIFFRACTION98
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)
16.502-1.5921-1.06599.0951-0.6933.30430.1360.65240.2526-0.4226-0.5736-0.74670.14981.49320.44980.21080.09780.04890.48330.04010.355940.6858-4.348518.9047
26.4901-1.12776.09131.3305-1.37068.89180.31020.242-0.4166-0.174-0.09090.08990.3825-0.0663-0.30230.2192-0.0014-0.00570.1416-0.0070.220619.3068-6.291516.4998
36.0916-5.085-4.73168.86280.99398.2926-0.1781-0.3831-1.32530.16740.072-0.46720.61820.45950.06910.23850.0549-0.00090.17110.03530.345727.8792-11.586424.0739
45.4662-0.10443.29080.86840.32645.12920.0696-0.3452-0.1185-0.0185-0.050.07330.0739-0.433-0.0290.140.01890.0210.09720.00590.154821.9146-0.929223.4289
57.5738-5.8359-1.85677.83072.86877.71750.18950.20290.7314-0.2824-0.2714-0.5531-1.050.32170.04180.292-0.01390.01290.13440.0560.235223.9659.405216.6745
66.4849-1.7072.70191.436-2.44276.22350.07310.10870.6379-0.2602-0.16620.6647-0.309-0.65780.08780.31820.21470.00740.3271-0.08090.26998.75257.884316.0508
76.3444.56416.29387.98485.89147.80820.0791-0.5230.23070.0062-0.31530.3203-0.3011-0.66250.2830.18290.06190.02460.2288-0.02220.186812.4685.800724.9567
83.0733-3.3587-0.16937.34134.1084.5310.1362-0.49670.9295-0.21530.4139-0.6795-0.37830.3144-0.38580.2267-0.00440.00660.2067-0.01530.245227.01298.405830.5586
97.3118-3.2197-1.32648.41945.91844.48580.43610.78760.1237-0.6889-0.2499-0.6158-0.43230.1398-0.31630.27110.04860.0810.30240.04950.247534.495-0.949712.3906
102.73053.6445-3.00936.1875-2.78744.4342-0.12641.1371-0.8029-0.52220.03160.2990.7393-0.33120.07130.38210.0619-0.02070.3757-0.13440.302125.0187-9.704611.6268
119.25084.81513.83768.9382-0.4623.29470.148-0.0034-0.6063-0.4781-0.3492-0.43610.22090.11510.29850.33370.09030.06220.26350.00780.224923.74440.76615.0856
123.675-0.6533-2.67987.02025.76868.1768-0.0910.255-0.0859-1.3278-0.37770.2015-0.674-0.53590.50490.48950.0922-0.03010.22480.02160.196116.42663.63693.2487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 169 )
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 186 )
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 196 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 4 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )

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