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

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Basic information

Entry
Database: PDB / ID: 7bmf
TitleCrystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with dCTP
ComponentsConserved protein
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 / inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain ...: / DHH-CID domain / inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / NITRATE ION / DI(HYDROXYETHYL)ETHER / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53219
Polymers101,4432
Non-polymers2,08917
Water3,711206
1
A: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,88111
Polymers50,7211
Non-polymers1,15910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6518
Polymers50,7211
Non-polymers9297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 53.880, 86.720
Angle α, β, γ (deg.)79.860, 82.770, 63.980
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Conserved protein / phosphodiesterase


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

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Non-polymers , 5 types, 223 molecules

#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-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M bis-Tris propane pH 6.5, 14% w/v PEG 3350, 0.2M sodium nitrate, 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.23 Å / Num. obs: 42571 / % possible obs: 97.6 % / Redundancy: 2 % / CC1/2: 0.942 / Net I/σ(I): 3.4
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3602 / CC1/2: 0.831

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Processing

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

6tvv


Resolution: 2.2→42.21 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.852 / SU B: 7.549 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 2785 5.1 %RANDOM
Rwork0.2535 ---
obs0.2558 42570 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.79 Å2 / Biso mean: 30.87 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.01 Å20.16 Å2
2--0.09 Å2-0.01 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.2→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 102 206 6799
Biso mean--37.61 30.92 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196687
X-RAY DIFFRACTIONr_bond_other_d0.0020.026246
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9859060
X-RAY DIFFRACTIONr_angle_other_deg1.124314288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0523.783267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.494151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471544
X-RAY DIFFRACTIONr_chiral_restr0.1260.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021472
LS refinement shellResolution: 2.21→2.27 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 186 -
Rwork0.324 3289 -
obs--82.02 %

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