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- PDB-4rg8: Structural and biochemical studies of a moderately thermophilic E... -

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Basic information

Entry
Database: PDB / ID: 4rg8
TitleStructural and biochemical studies of a moderately thermophilic Exonuclease I from Methylocaldum szegediense
ComponentsExonuclease I
KeywordsHYDROLASE / Methylocaldum szegediense / Exonuclease / DNA binding protein
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Helix Hairpins - #1240 / Exonuclease ExoI, domain 3 / Exonuclease ExoI, domain 2 / Exodeoxyribonuclease I, C-terminal / Exodeoxyribonuclease I / Exonuclease I, SH3-like domain / Exonuclease I, C-terminal alpha-helical domain / Exonuclease I, SH3-like domain superfamily / Exonuclease C-terminal / Exonuclease I (ExoI) SH3-like domain profile. ...Helix Hairpins - #1240 / Exonuclease ExoI, domain 3 / Exonuclease ExoI, domain 2 / Exodeoxyribonuclease I, C-terminal / Exodeoxyribonuclease I / Exonuclease I, SH3-like domain / Exonuclease I, C-terminal alpha-helical domain / Exonuclease I, SH3-like domain superfamily / Exonuclease C-terminal / Exonuclease I (ExoI) SH3-like domain profile. / Exonuclease I (ExoI) C-terminal domain profile. / PX Domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Monooxygenase / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Exodeoxyribonuclease I
Similarity search - Component
Biological speciesMethylocaldum szegediense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsFei, L. / Tian, S. / Moysey, R. / Misca, M. / Barker, J.J. / Smith, M.A. / McEwan, P.A. / Pilka, E.S. / Crawley, L. / Evans, T. / Sun, D.
CitationJournal: Plos One / Year: 2015
Title: Structural and Biochemical Studies of a Moderately Thermophilic Exonuclease I from Methylocaldum szegediense.
Authors: Fei, L. / Tian, S. / Moysey, R. / Misca, M. / Barker, J.J. / Smith, M.A. / McEwan, P.A. / Pilka, E.S. / Crawley, L. / Evans, T. / Sun, D.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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 / 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_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.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_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: Exonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2992
Polymers59,2751
Non-polymers241
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.967, 97.020, 111.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exonuclease I


Mass: 59275.043 Da / Num. of mol.: 1 / Fragment: Exonuclease I / Mutation: NONE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylocaldum szegediense (bacteria) / Gene: Exonuclease I / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A0R5X6*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG6K, 0.1 M Tris pH8, 0.2 M calcium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.12→29.08 Å / Num. all: 36277 / Num. obs: 36277 / % possible obs: 99.22 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.12-2.17194.92
2.12-29.08199.22

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FXX

1fxx


Resolution: 2.12→29.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.618 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25292 1912 5 %RANDOM
Rwork0.22278 ---
all0.22278 ---
obs0.22433 36277 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0 Å2
2--0.44 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 1 189 3958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193910
X-RAY DIFFRACTIONr_bond_other_d0.0010.023772
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9765318
X-RAY DIFFRACTIONr_angle_other_deg0.74138653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70222.338201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2391554
X-RAY DIFFRACTIONr_chiral_restr0.0590.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
X-RAY DIFFRACTIONr_mcbond_it1.5554.8611884
X-RAY DIFFRACTIONr_mcbond_other1.5554.861883
X-RAY DIFFRACTIONr_mcangle_it2.6247.2792355
X-RAY DIFFRACTIONr_mcangle_other2.6237.2812356
X-RAY DIFFRACTIONr_scbond_it1.5965.0492026
X-RAY DIFFRACTIONr_scbond_other1.5965.0492026
X-RAY DIFFRACTIONr_scangle_other2.7557.4982957
X-RAY DIFFRACTIONr_long_range_B_refined4.95938.1544530
X-RAY DIFFRACTIONr_long_range_B_other4.80438.1154479
LS refinement shellResolution: 2.115→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 128 -
Rwork0.336 2523 -
obs--94.92 %

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