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- PDB-4e19: Crystal structure of RNase H1 from halophilic archaeon Halobacter... -

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Basic information

Entry
Database: PDB / ID: 4.0E+19
TitleCrystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1
Componentsribonuclease H1
KeywordsHYDROLASE / RNase H1
Function / homology
Function and homology information


exonuclease activity / ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Reverse transcriptase-like / Ribonuclease H-like superfamily/Ribonuclease H / 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
Biological speciesHalobacterium salinarium (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsYou, D.J. / Angkawidjaja, C. / Koga, Y. / Kanaya, S.
CitationJournal: To be Published
Title: Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1
Authors: You, D.J. / Angkawidjaja, C. / Koga, Y. / Kanaya, S.
History
DepositionMar 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_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_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.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_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

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Assembly

Deposited unit
A: ribonuclease H1
B: ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2787
Polymers42,0042
Non-polymers2755
Water5,459303
1
A: ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1123
Polymers21,0021
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1674
Polymers21,0021
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.802, 115.802, 38.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein ribonuclease H1


Mass: 21001.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarium (Halophile) / Strain: NRC-1 / Gene: VNG_0255C / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9HSF6, ribonuclease H
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(W/V) PEG 8000, Imidazole(pH6.5), 3%(V/V) MPD, 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: BRUKER SMART 6500 / Detector: CCD / Date: Oct 10, 2011
Diffraction measurementDetails: 1.00 degrees, 0.7 sec, detector distance 150.00 mm / Method: \w scans
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionAv R equivalents: 0.074 / Number: 362644
ReflectionResolution: 1.41→50 Å / Num. obs: 48997 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 31.61
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.613 / Rsym value: 0.381 / % possible all: 98.9
Cell measurementReflection used: 362644

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.64 Å40.94 Å
Translation1.64 Å40.94 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 41564
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.07-10026.10.674514
4.76-6.0723.40.872598
4.04-4.76220.902780
3.57-4.0424.80.902856
3.24-3.5730.10.889940
2.98-3.2430.20.871989
2.78-2.9831.90.8551065
2.61-2.7829.40.8661132
2.47-2.61290.8771223
2.35-2.4728.80.8711244
2.25-2.3530.20.8771352
2.16-2.2527.50.8761343
2.08-2.1628.90.871453
2-2.0827.80.8691442
1.94-228.90.8771560
1.88-1.9430.20.8711563
1.82-1.8831.60.8751599
1.77-1.8232.70.8841721
1.73-1.7732.80.8771683
1.69-1.7333.30.8711740
1.65-1.6934.30.871805
1.61-1.6534.20.8841800
1.58-1.6133.40.8851865
1.54-1.5834.10.8751818
1.51-1.5435.20.871901
1.48-1.5138.50.8641921
1.46-1.4841.60.842019
1.41-1.46490.8083638

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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
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EHG

2ehg


Resolution: 1.41→40.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.907 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2472 5.1 %RANDOM
Rwork0.1717 ---
all0.1734 ---
obs0.1734 48893 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.16 Å2 / Biso mean: 18.1282 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å2-0 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 5 303 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212028
X-RAY DIFFRACTIONr_angle_refined_deg2.411.9382757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59724110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83515294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2141522
X-RAY DIFFRACTIONr_chiral_restr0.1560.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211638
X-RAY DIFFRACTIONr_mcbond_it1.5431.51302
X-RAY DIFFRACTIONr_mcangle_it2.52922047
X-RAY DIFFRACTIONr_scbond_it3.573726
X-RAY DIFFRACTIONr_scangle_it5.4944.5710
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.412-1.4480.2651580.2223360357298.488
1.448-1.4880.231840.1983309350499.686
1.488-1.5310.2311620.1743274344199.855
1.531-1.5780.2061580.1633136330399.728
1.578-1.630.1961700.1573017319899.656
1.63-1.6870.2371610.1642973314199.777
1.687-1.7510.1941350.1572871301499.735
1.751-1.8220.181690.1572737291299.794
1.822-1.9030.1981460.1642619277199.783
1.903-1.9960.1881370.172521266399.812
1.996-2.1040.2181180.182408252899.921
2.104-2.2310.211210.1652271239799.791
2.231-2.3850.2011090.1732149226099.912
2.385-2.5760.2221240.1871979210699.858
2.576-2.8220.22990.1881841194299.897
2.822-3.1550.24980.1891676177799.831
3.155-3.6420.219810.161465155299.613
3.642-4.4580.17530.1451278133699.626
4.458-6.2950.162580.165991105199.81
6.295-81.8840.207310.20454660196.007

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