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- PDB-5swm: BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER F... -

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Basic information

Entry
Database: PDB / ID: 5swm
TitleBACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRID
Components
  • DNA (12-MER)
  • RNA (12-MER)
  • Ribonuclease H
KeywordsHYDROLASE/RNA/DNA / RNASE H / RNA/DNA HYBRID / 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM055237 United States
CitationJournal: Biochemistry / Year: 2016
Title: Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.
Authors: Pallan, P.S. / Prakash, T.P. / de Leon, A.R. / Egli, M.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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: Ribonuclease H
C: RNA (12-MER)
D: DNA (12-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4798
Polymers40,2224
Non-polymers2574
Water4,954275
1
A: Ribonuclease H
C: RNA (12-MER)
D: DNA (12-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1507
Polymers23,8933
Non-polymers2574
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease H
C: RNA (12-MER)
D: DNA (12-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9854
Polymers23,8933
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.474, 44.500, 62.174
Angle α, β, γ (deg.)84.42, 89.90, 65.10
Int Tables number1
Space group name H-MP1

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Components

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Protein / RNA chain / DNA chain , 3 types, 4 molecules ABCD

#1: Protein Ribonuclease H / / RNase H


Mass: 16329.478 Da / Num. of mol.: 2 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA / Plasmid: PET15B / Production host: BACILLUS HALODURANS (bacteria) / Strain (production host): BL21 PLYSS / References: UniProt: Q9KEI9, ribonuclease H
#2: RNA chain RNA (12-MER)


Mass: 3796.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (12-MER)


Mass: 3767.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 279 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.27 Å3/Da / Density % sol: 45.84 % / Description: Crystals with medium thickness
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.4 M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91836 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 1.5→26.6 Å / Num. obs: 55661 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 46
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 10.6 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1ZBI

1zbi


Resolution: 1.5→26.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.194 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2680 4.8 %RANDOM
Rwork0.161 ---
obs0.162 52981 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0.16 Å2-0.04 Å2
2--0.21 Å20.18 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 495 15 275 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0183853
X-RAY DIFFRACTIONr_bond_other_d0.0010.022855
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.9955531
X-RAY DIFFRACTIONr_angle_other_deg0.9936663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16824.84597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4381510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.023197
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.0021054
X-RAY DIFFRACTIONr_mcbond_other1.3060.9991053
X-RAY DIFFRACTIONr_mcangle_it1.9351.51314
X-RAY DIFFRACTIONr_mcangle_other1.9351.5031315
X-RAY DIFFRACTIONr_scbond_it2.07512799
X-RAY DIFFRACTIONr_scbond_other2.07512799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9741.4374218
X-RAY DIFFRACTIONr_long_range_B_refined5.87311.5654645
X-RAY DIFFRACTIONr_long_range_B_other5.87611.5694646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 140 -
Rwork0.153 2985 -
obs--72.29 %
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)
10.7533-0.2272-0.22581.6139-0.41712.0927-0.0778-0.05560.0062-0.02630.0460.02340.04470.00580.03180.01330.0108-0.00390.0147-0.00350.01950.449-0.3179-0.4155
20.75260.24550.19761.6363-0.37362.033-0.07380.0506-0.01340.02860.04460.0236-0.0410.00260.02920.01-0.00590.00480.0082-0.00510.0131-18.2683-3.929940.3971
30.0002-0.0017-0.00520.12-0.02870.2513-0.00340.0006-0.00090.0324-0.05080.01840.0521-0.00510.05430.03630.00150.00680.09340.00110.05362.6335-2.07220.0258
40.00040.00090.00290.00250.01090.09260.00680.00040.00010.01030.0072-0.00420.03070.0968-0.0140.05470.00440.00540.14170.01910.08314.2083-2.10720.0217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 193
2X-RAY DIFFRACTION2B62 - 194
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12

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