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- PDB-7bhi: Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoau... -

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Basic information

Entry
Database: PDB / ID: 7bhi
TitleCrystal structure of RecJ-Cdc45 from Methanothermobacter Thermoautotrophicus
ComponentsConserved protein
KeywordsDNA BINDING PROTEIN / phosphodiesterase / dna binding / cdc45 homologue
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
: / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDe March, M. / Onesti, S.
CitationJournal: To Be Published
Title: Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoautotrophicus
Authors: De March, M. / Onesti, S.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Conserved protein
B: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6636
Polymers101,4432
Non-polymers2204
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-25 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.471, 55.010, 89.990
Angle α, β, γ (deg.)81.380, 86.360, 89.950
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 13 - 455 / Label seq-ID: 13 - 455

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

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Components

#1: Protein Conserved 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris/HCl pH 8.5, 27% w/v PEG 4000, 0.2M MgCl2*6H20, 1mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.7→88.79 Å / Num. obs: 19511 / % possible obs: 92.8 % / Redundancy: 1.7 % / CC1/2: 0.97 / Net I/σ(I): 3.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 1.6 % / Num. unique obs: 2782 / CC1/2: 0.83 / % possible all: 90.4

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Processing

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

6tvv


Resolution: 2.7→88.79 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.853 / SU B: 18.331 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 1012 5.2 %RANDOM
Rwork0.2305 ---
obs0.2326 18487 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 30.098 Å2 / Biso min: 3.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0.75 Å2-0.23 Å2
2--0.67 Å21.35 Å2
3---1.33 Å2
Refinement stepCycle: final / Resolution: 2.7→88.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 4 38 6335
Biso mean--30.19 18.74 -
Num. residues----884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196403
X-RAY DIFFRACTIONr_bond_other_d0.0030.025889
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9688710
X-RAY DIFFRACTIONr_angle_other_deg1.113313426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66123.702235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45615917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1591533
X-RAY DIFFRACTIONr_chiral_restr0.0780.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027492
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021423
Refine LS restraints NCS

Ens-ID: 1 / Number: 45530 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 71 -
Rwork0.274 1304 -
all-1375 -
obs--89.69 %

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