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- PDB-4aby: Crystal structure of Deinococcus radiodurans RecN head domain -

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Basic information

Entry
Database: PDB / ID: 4aby
TitleCrystal structure of Deinococcus radiodurans RecN head domain
ComponentsDNA REPAIR PROTEIN RECN
KeywordsHYDROLASE / DNA REPAIR / DOUBLE STRAND BREAK REPAIR / ATPASE / NUCLEOTIDE BINDING DOMAIN
Function / homology
Function and homology information


bacterial nucleoid / SOS response / DNA recombination / DNA repair / ATP binding / identical protein binding
Similarity search - Function
DNA recombination/repair protein RecN / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair protein RecN
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsPellegrino, S. / Radzimanowski, J. / de Sanctis, D. / McSweeney, S. / Timmins, J.
CitationJournal: Structure / Year: 2012
Title: Structural and Functional Characterization of an Smc-Like Protein Recn: New Insights Into Double-Strand Break Repair.
Authors: Pellegrino, S. / Radzimanowski, J. / De Sanctis, D. / Erba, E.B. / Mcsweeney, S. / Timmins, J.
History
DepositionDec 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN RECN
B: DNA REPAIR PROTEIN RECN
C: DNA REPAIR PROTEIN RECN
D: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)177,1654
Polymers177,1654
Non-polymers00
Water1,838102
1
A: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)44,2911
Polymers44,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)44,2911
Polymers44,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)44,2911
Polymers44,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)44,2911
Polymers44,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.863, 61.986, 133.824
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -0.0017, -0.002), (0.0017, -0.9999, 0.012), (-0.002, 0.012, 0.9999)165.4235, 32.1416, -0.0868
3given(-0.5454, 0.472, 0.6926), (-0.4603, -0.8593, 0.223), (0.7004, -0.1972, 0.686)143.164, 98.2365, 1.3476
4given(0.4906, -0.6051, 0.627), (0.4333, 0.7937, 0.4269), (-0.756, 0.0623, 0.6516)73.6821, -12.2188, 113.077

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Components

#1: Protein
DNA REPAIR PROTEIN RECN / RECN / RECOMBINATION PROTEIN N


Mass: 44291.133 Da / Num. of mol.: 4 / Fragment: HEAD DOMAIN, RESIDUES 1-195,365-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q9WXF2, EC: 3.6.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPEPTIDE LINKER ESSKHPTSLVPRGS INSERTED IN BETWEEN N AND C- TERMINAL DOMAINS

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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: 3.13 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: TRIS 0.1 M PH 7.5, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→82.3 Å / Num. obs: 41994 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3→49.51 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2117 5 %
Rwork0.2095 --
obs0.2115 41983 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.73 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 43.49 Å2
Baniso -1Baniso -2Baniso -3
1--9.4974 Å20 Å2-1.9953 Å2
2--8.3617 Å20 Å2
3---1.1357 Å2
Refinement stepCycle: LAST / Resolution: 3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10345 0 0 102 10447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410456
X-RAY DIFFRACTIONf_angle_d0.78514130
X-RAY DIFFRACTIONf_dihedral_angle_d16.163779
X-RAY DIFFRACTIONf_chiral_restr0.0531669
X-RAY DIFFRACTIONf_plane_restr0.0021841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9997-3.10690.31942180.28093972X-RAY DIFFRACTION100
3.1069-3.23130.31932100.26283939X-RAY DIFFRACTION100
3.2313-3.37830.27931810.2374010X-RAY DIFFRACTION100
3.3783-3.55640.26192010.21393958X-RAY DIFFRACTION100
3.5564-3.77910.25431980.19494003X-RAY DIFFRACTION100
3.7791-4.07080.21252150.18414013X-RAY DIFFRACTION100
4.0708-4.48020.21632280.17443999X-RAY DIFFRACTION100
4.4802-5.12790.2192360.17473968X-RAY DIFFRACTION100
5.1279-6.45840.24322150.20463979X-RAY DIFFRACTION99
6.4584-49.51650.242150.21514025X-RAY DIFFRACTION97

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