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- PDB-3zbo: A new family of proteins related to the HEAT-like repeat DNA glyc... -

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Basic information

Entry
Database: PDB / ID: 3zbo
TitleA new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures
ComponentsALKF
KeywordsUNKNOWN FUNCTION / DNA DAMAGE / BASE EXCISION REPAIR / ALKC / ALKD / HOLLIDAY JUNCTIONS
Function / homologyDNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / DNA alkylation repair protein
Function and homology information
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsBacke, P.H. / Simm, R. / Laerdahl, J.K. / Dalhus, B. / Fagerlund, A. / Okstad, O.A. / Rognes, T. / Alseth, I. / Kolsto, A.-B. / Bjoras, M.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: A New Family of Proteins Related to the Heat-Like Repeat DNA Glycosylases with Affinity for Branched DNA Structures.
Authors: Backe, P.H. / Simm, R. / Laerdahl, J.K. / Dalhus, B. / Fagerlund, A. / Okstad, O.A. / Rognes, T. / Alseth, I. / Kolsto, A.-B. / Bjoras, M.
History
DepositionNov 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ALKF
B: ALKF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2033
Polymers54,1682
Non-polymers351
Water11,926662
1
A: ALKF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1192
Polymers27,0841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALKF


Theoretical massNumber of molelcules
Total (without water)27,0841
Polymers27,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.921, 87.159, 112.604
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 ALKF


Mass: 27083.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q81BA8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.4 Å3/Da / Density % sol: 48.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
DetectorType: MARRESEARCH SX-165 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 68454 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.97
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.76 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T06

1t06


Resolution: 1.58→25.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.342 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20452 3629 5 %RANDOM
Rwork0.16491 ---
obs0.16692 68454 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.58→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 1 662 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2631.9615364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6324.693179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1111521
X-RAY DIFFRACTIONr_chiral_restr0.1530.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022963
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4221.52420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34823911
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.73631542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.054.51426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.578→1.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 256 -
Rwork0.245 4841 -
obs--96.61 %

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