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- PDB-4ly7: Ancestral RNase H -

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Basic information

Entry
Database: PDB / ID: 4ly7
TitleAncestral RNase H
ComponentsRibonuclease H
KeywordsHYDROLASE / ribonuclease
Function / homologyRibonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsHart, K.M. / Harms, M.J. / Schmidt, B.H. / Elya, C. / Thornton, J.W. / Marqusee, S.
CitationJournal: Plos Biol. / Year: 2014
Title: Thermodynamic system drift in protein evolution.
Authors: Hart, K.M. / Harms, M.J. / Schmidt, B.H. / Elya, C. / Thornton, J.W. / Marqusee, S.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Sep 20, 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
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8023
Polymers17,6101
Non-polymers1922
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.379, 82.379, 44.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Ribonuclease H


Mass: 17609.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Description: Ancestral Sequence Reconstruction (ASR) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 30mM lithium sulfate, 1mM TCEP, 100mM Bis-Tris pH 6.5, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2012
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.36→41.189 Å / Num. all: 37239 / Num. obs: 37194 / % possible obs: 99.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 13.24 Å2 / Rsym value: 0.079 / Net I/σ(I): 26.1
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.858 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
PHASERphasing
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RN2

2rn2


Resolution: 1.36→41.189 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 15.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1559 1853 4.99 %
Rwork0.1263 --
obs0.1279 37171 99.87 %
all-37239 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→41.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 10 220 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131379
X-RAY DIFFRACTIONf_angle_d1.3291885
X-RAY DIFFRACTIONf_dihedral_angle_d15.116520
X-RAY DIFFRACTIONf_chiral_restr0.086192
X-RAY DIFFRACTIONf_plane_restr0.008250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3603-1.39710.24151450.20252707X-RAY DIFFRACTION99
1.3971-1.43820.23921400.17162672X-RAY DIFFRACTION100
1.4382-1.48460.20461420.15322704X-RAY DIFFRACTION100
1.4846-1.53760.20321390.13072708X-RAY DIFFRACTION100
1.5376-1.59920.1671390.1112695X-RAY DIFFRACTION100
1.5992-1.6720.14441420.10612715X-RAY DIFFRACTION100
1.672-1.76020.13771460.11072699X-RAY DIFFRACTION100
1.7602-1.87040.16211410.10892730X-RAY DIFFRACTION100
1.8704-2.01480.13831440.10942704X-RAY DIFFRACTION100
2.0148-2.21760.14611410.10352721X-RAY DIFFRACTION100
2.2176-2.53840.13261450.11532731X-RAY DIFFRACTION100
2.5384-3.1980.15511480.12852741X-RAY DIFFRACTION100
3.198-41.20840.15361410.14252791X-RAY DIFFRACTION100

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