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- PDB-3vn5: Crystal structure of Aquifex aeolicus RNase H3 -

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Basic information

Entry
Database: PDB / ID: 3vn5
TitleCrystal structure of Aquifex aeolicus RNase H3
ComponentsRibonuclease HIII
KeywordsHYDROLASE / RNase H3
Function / homology
Function and homology information


ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease HIII, N-terminal / Ribonuclease HIII / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 ...Ribonuclease HIII, N-terminal / Ribonuclease HIII / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily / 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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsJongruja, N. / You, D.J. / Eiko, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: Febs J. / Year: 2012
Title: Structure and characterization of RNase H3 from Aquifex aeolicus
Authors: Jongruja, N. / You, D.J. / Angkawidjaja, C. / Kanaya, E. / Koga, Y. / Kanaya, S.
History
DepositionDec 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease HIII


Theoretical massNumber of molelcules
Total (without water)29,5851
Polymers29,5851
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.943, 48.943, 293.217
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ribonuclease HIII / RNase HIII


Mass: 29584.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1768, rnhC / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC 2067 (DE3) / References: UniProt: O67644, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M citrate buffer (pH 4.0), 0.2M sodium citrate, 20% w/v polyethylene glycol (PEG) 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 29839 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.98-2.0121.40.2891100
2.01-2.0522.10.261100
2.05-2.0921.90.2291100
2.09-2.1321.90.2091100
2.13-2.18220.1871100
2.18-2.2321.90.1811100
2.23-2.2922.10.161100
2.29-2.3521.80.1491100
2.35-2.42220.1381100
2.42-2.4921.70.1321100
2.49-2.5822.10.1231100
2.58-2.6921.70.1151100
2.69-2.8121.80.1061100
2.81-2.9621.70.0971100
2.96-3.1421.60.0921100
3.14-3.3921.50.098199.9
3.39-3.7320.70.11199.9
3.73-4.26190.103199.9
4.26-5.3719.40.086199.7
5.37-5018.70.06199.9

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Phasing

PhasingMethod: molecular replacement
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13814
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.92-10031.70.766501
4.76-5.9232.10.909506
4.19-4.7633.60.927505
3.83-4.1940.40.931508
3.57-3.8342.10.94502
3.36-3.5746.30.928503
3.2-3.36450.928510
3.05-3.242.50.923513
2.92-3.0542.50.917508
2.82-2.9239.80.91509
2.72-2.8240.40.905516
2.64-2.72420.922555
2.56-2.6439.80.925516
2.49-2.5639.90.93544
2.43-2.4938.40.911547
2.37-2.4338.10.924601
2.31-2.3741.10.933558
2.26-2.3140.10.939625
2.21-2.2639.70.938563
2.17-2.21440.929599
2.12-2.1738.60.938627
2.08-2.1239.10.933638
2.05-2.0838.40.93624
1.98-2.0546.50.9221236

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6.1phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D0A

2d0a


Resolution: 1.98→48.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.757 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23844 1504 5.1 %RANDOM
Rwork0.20434 ---
obs0.20603 28119 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å2-0 Å2
2--0.49 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.98→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 103 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0492.0012828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06324.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13615421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2531512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211526
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9251.51273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.21222061
X-RAY DIFFRACTIONr_scbond_it5.1093831
X-RAY DIFFRACTIONr_scangle_it8.2594.5767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.981-2.0320.221960.22220480.222217398.6650.194
2.032-2.0880.2821200.20419460.209207599.5660.178
2.088-2.1490.231130.19519130.197203599.5580.172
2.149-2.2150.2511050.218760.203198899.6480.179
2.215-2.2870.215970.20118120.202191799.5830.18
2.287-2.3680.2221000.19617570.198186599.5710.178
2.368-2.4570.256820.22617340.227182699.4520.206
2.457-2.5570.271910.22316310.226172999.5950.207
2.557-2.6710.328920.23615860.241168499.6440.216
2.671-2.8010.263640.23715340.238160399.6880.224
2.801-2.9520.28670.24814410.249151699.4720.235
2.952-3.1310.24590.23113950.231145899.7260.223
3.131-3.3470.262910.22112840.223138499.350.22
3.347-3.6150.244830.19511960.198128399.6880.197
3.615-3.960.156520.18311420.182119899.6660.189
3.96-4.4260.184550.15110530.153111599.3720.164
4.426-5.1090.23470.1699100.17296099.6880.183
5.109-6.2530.254430.2018150.20385999.8840.213
6.253-8.8250.183270.1866460.18667699.5560.207
8.825-97.7390.215200.2084000.20842499.0570.255

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