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- PDB-2etj: Crystal structure of Ribonuclease HII (EC 3.1.26.4) (RNase HII) (... -

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Basic information

Entry
Database: PDB / ID: 2etj
TitleCrystal structure of Ribonuclease HII (EC 3.1.26.4) (RNase HII) (tm0915) from THERMOTOGA MARITIMA at 1.74 A resolution
ComponentsRibonuclease HII
KeywordsHYDROLASE / tm0915 / Ribonuclease HII (EC 3.1.26.4) (RNase HII) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease HII / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ribonuclease HII (EC 3.1.26.4) (RNase HII) (tm0915) from THERMOTOGA MARITIMA at 1.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease HII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7848
Polymers28,4141
Non-polymers3707
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.821, 51.821, 76.293
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Ribonuclease HII / RNase HII


Mass: 28414.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rnhB / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X017, ribonuclease H
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.8
Details: 0.2M MgCl2, 20.0% PEG-3350, No Buffer , pH 5.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9797, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 29, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
211
ReflectionResolution: 1.74→18.15 Å / Num. obs: 23391 / % possible obs: 99.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.74-1.7999.52.80.4691.517400.469
1.79-1.8399.82.80.3941.816780.394
1.83-1.8999.42.80.3721.916140.372
1.89-1.9599.52.80.228316090.228
1.95-2.0199.62.80.1853.815830.185
2.01-2.0899.52.80.1464.414700.146
2.08-2.1699.72.80.1255.514390.125
2.16-2.2599.52.80.1135.914190.113
2.25-2.3599.72.80.1066.513110.106
2.35-2.4699.52.80.0818.712650.081
2.46-2.5999.82.80.0759.212310.075
2.59-2.7599.72.80.0699.611300.069
2.75-2.9499.92.80.06310.510770.063
2.94-3.1899.92.80.05611.910050.056
3.18-3.4899.72.80.05311.89310.053
3.48-3.8999.82.80.0512.98280.05
3.89-4.4999.72.80.04514.17290.045
4.49-5.599.52.70.047136240.047
5.5-7.7898.62.70.05212.34830.052
7.78-18.1585.12.50.048142250.048

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→18.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.952 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1194 5.1 %RANDOM
Rwork0.179 ---
all0.182 ---
obs-22167 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.215 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.74→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 22 161 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221674
X-RAY DIFFRACTIONr_bond_other_d0.0020.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9872246
X-RAY DIFFRACTIONr_angle_other_deg0.95932867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63923.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5381513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2150.2360
X-RAY DIFFRACTIONr_nbd_other0.2030.21269
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2793
X-RAY DIFFRACTIONr_nbtor_other0.090.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.29
X-RAY DIFFRACTIONr_mcbond_it2.51331092
X-RAY DIFFRACTIONr_mcbond_other0.6083431
X-RAY DIFFRACTIONr_mcangle_it3.21651680
X-RAY DIFFRACTIONr_scbond_it6.1148656
X-RAY DIFFRACTIONr_scangle_it8.16711566
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 86 -
Rwork0.23 1650 -
obs--99.31 %
Refinement TLS params.Method: refined / Origin x: 14.3853 Å / Origin y: 8.1884 Å / Origin z: 3.9748 Å
111213212223313233
T-0.0846 Å20.0078 Å2-0.0147 Å2--0.007 Å20.0203 Å2---0.0677 Å2
L1.7344 °20.0144 °2-0.5758 °2-0.7987 °20.421 °2--0.9833 °2
S-0.0456 Å °-0.0483 Å °-0.1762 Å °0.0504 Å °-0.0161 Å °0.0593 Å °0.0455 Å °-0.0402 Å °0.0617 Å °
Refinement TLS groupSelection: all

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