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- PDB-3u3g: Structure of LC11-RNase H1 Isolated from Compost by Metagenomic A... -

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Basic information

Entry
Database: PDB / ID: 3u3g
TitleStructure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into the Structural Bases for Unusual Enzymatic Properties of Sto-RNase H1
ComponentsRibonuclease H
KeywordsHYDROLASE / Cleave the RNA strand of RNA/DNA hybrid
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding
Similarity search - Function
Reverse transcriptase-like / Ribonuclease H-like superfamily/Ribonuclease H / 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
Unknown ligand / Ribonuclease H
Similarity search - Component
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNguyen, T.N. / Angkawidjaja, C. / Kanaya, E. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1
Authors: Nguyen, T.N. / Angkawidjaja, C. / Kanaya, E. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Ribonuclease H
B: Ribonuclease H
C: Ribonuclease H
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5997
Polymers62,5284
Non-polymers713
Water16,286904
1
D: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,6321
Polymers15,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,6321
Polymers15,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6672
Polymers15,6321
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6673
Polymers15,6321
Non-polymers352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.315, 104.891, 57.212
Angle α, β, γ (deg.)90.00, 110.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease H / RNase H1


Mass: 15631.940 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: E0X767, ribonuclease H
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 49.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole, 0.2M sodium cloride, 0.4M sodium dihydrogen phosphate, 1.6M dipotassium phosphate, pH 8, VAPOR DIFFUSION, SITTING 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 115103 / % possible obs: 97.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.051 / Net I/σ(I): 31.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5082 / Rsym value: 0.422 / % possible all: 85.8

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Processing

Software
NameVersionClassification
BL44XUBSSdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H08

3h08


Resolution: 1.4→47.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.885 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19204 5756 5 %RANDOM
Rwork0.17219 ---
obs0.17319 109228 97.61 %-
all-117805 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 11 904 5291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9826062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35825.362207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0611528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0213343
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_it1.6911.52807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.88224545
X-RAY DIFFRACTIONr_scbond_it4.9431682
X-RAY DIFFRACTIONr_scangle_it7.7964.51509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 403 -
Rwork0.258 7545 -
obs--91.31 %

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