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- PDB-7bjq: Crystal structure of RecJCdc45 from Methanothermobacter thermoaut... -

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Basic information

Entry
Database: PDB / ID: 7bjq
TitleCrystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with ssDNA
Components
  • Conserved proteinConservation
  • DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
KeywordsDNA BINDING PROTEIN / phosphodiesterase
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding / nucleotide binding / metal ion binding
Similarity search - Function
: / DHH-CID domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
: / DNA / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDe March, M. / Onesti, S.
CitationJournal: To Be Published
Title: Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus
Authors: De March, M. / Onesti, S.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved protein
B: Conserved protein
D: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
E: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
F: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
G: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,89910
Polymers108,6806
Non-polymers2204
Water70339
1
A: Conserved protein
F: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
G: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4505
Polymers54,3403
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-22 kcal/mol
Surface area19910 Å2
MethodPISA
2
B: Conserved protein
D: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
E: DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4505
Polymers54,3403
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-19 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.080, 69.501, 72.210
Angle α, β, γ (deg.)86.120, 69.260, 69.530
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Conserved protein / Conservation / Phosphodiesterase / DHHA1 domain-containing protein


Mass: 50721.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_1422 / Production host: Escherichia coli (E. coli) / References: UniProt: O27473
#2: DNA chain
DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')


Mass: 1809.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M bis-Tris pH 5.5, 17% w/v PEG 10000, 1M NH4CH3CO2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→67.39 Å / Num. obs: 11350 / % possible obs: 98.1 % / Redundancy: 3.1 % / CC1/2: 0.984 / Net I/σ(I): 9.6
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3804 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TVV

6tvv


Resolution: 2.7→67.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.625 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1462 5.1 %RANDOM
Rwork0.1963 ---
obs0.1997 10315 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 205.17 Å2 / Biso mean: 62.605 Å2 / Biso min: 29.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20.21 Å2-1.35 Å2
2---3.87 Å2-0.69 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 2.7→67.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 492 4 39 7031
Biso mean--93.73 49.42 -
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197160
X-RAY DIFFRACTIONr_bond_other_d0.0020.026436
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9019813
X-RAY DIFFRACTIONr_angle_other_deg1.187314721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5895888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20623.569269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.877151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7231545
X-RAY DIFFRACTIONr_chiral_restr0.0960.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021622
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 113 -
Rwork0.328 2027 -
all-2140 -
obs--96.66 %

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