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- PDB-6tvv: Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii -

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Basic information

Entry
Database: PDB / ID: 6tvv
TitleCrystal structure of 3'-5' RecJ exonuclease from M. Jannaschii
ComponentsMjaRecJ
KeywordsDNA BINDING PROTEIN / RecJ / exonuclease / DNA recombination and repair / archaea / resolution
Function / homology
Function and homology information


single-stranded DNA 5'-3' DNA exonuclease activity / DNA recombination / nucleic acid binding
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) - #30 / : / inorganic pyrophosphatase (n-terminal core) / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein MJ0831
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsDe March, M. / Medagli, B. / Krastanova, I. / Saha, I. / Pisani, F. / Onesti, S.
CitationJournal: To Be Published
Title: Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii
Authors: De March, M. / Medagli, B. / Krastanova, I. / Saha, I. / Pisani, F. / Onesti, S.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MjaRecJ
B: MjaRecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3089
Polymers97,8122
Non-polymers4967
Water23413
1
A: MjaRecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2926
Polymers48,9061
Non-polymers3865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MjaRecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0163
Polymers48,9061
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-37 kcal/mol
Surface area35740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.070, 92.070, 275.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 426 / Label seq-ID: 1 - 427

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein MjaRecJ


Mass: 48905.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58241
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium citrate, 0.1 M Bis-Tris-Propane pH 8.5, 14-24 % w/v PEG 3350, 10 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.89113 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89113 Å / Relative weight: 1
ReflectionResolution: 2.8→99.9 Å / Num. obs: 30267 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4308 / CC1/2: 0.378

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→87.33 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.909 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.867 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26389 1476 4.9 %RANDOM
Rwork0.2145 ---
obs0.21683 28682 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.281 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--1.82 Å20 Å2
3----3.65 Å2
Refinement stepCycle: 1 / Resolution: 2.8→87.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 22 13 6373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175967
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6228785
X-RAY DIFFRACTIONr_angle_other_deg1.341.57313700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5045856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35123.759266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.106151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.511518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021291
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_it4.8465.6553430
X-RAY DIFFRACTIONr_mcbond_other4.8465.6553429
X-RAY DIFFRACTIONr_mcangle_it7.0258.4924284
X-RAY DIFFRACTIONr_mcangle_other7.0258.4934285
X-RAY DIFFRACTIONr_scbond_it5.2825.9653043
X-RAY DIFFRACTIONr_scbond_other5.2815.9653044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9648.7594502
X-RAY DIFFRACTIONr_long_range_B_refined10.21767.0116997
X-RAY DIFFRACTIONr_long_range_B_other10.21667.0166998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12040 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 117 -
Rwork0.31 2064 -
obs--100 %

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