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- PDB-4abx: Crystal structure of Deinococcus radiodurans RecN coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 4abx
TitleCrystal structure of Deinococcus radiodurans RecN coiled-coil domain
ComponentsDNA REPAIR PROTEIN RECN
KeywordsDNA BINDING PROTEIN / ATP BINDING PROTEIN / DNA REPAIR / DOUBLE STRAND BREAK REPAIR / COILED-COIL
Function / homology
Function and homology information


SOS response / response to radiation / DNA recombination / DNA repair / ATP binding / identical protein binding
Similarity search - Function
Helix Hairpins - #1080 / Helix Hairpins - #1090 / DNA recombination/repair protein RecN / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Helix Hairpins / Helix non-globular / Special / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RecN
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.041 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 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)74,2254
Polymers74,2254
Non-polymers00
Water8,089449
1
A: DNA REPAIR PROTEIN RECN
D: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)37,1132
Polymers37,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-37.7 kcal/mol
Surface area19240 Å2
MethodPISA
2
B: DNA REPAIR PROTEIN RECN
C: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)37,1132
Polymers37,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-37 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.210, 43.970, 133.630
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18556.266 Da / Num. of mol.: 4 / Fragment: COILED-COIL DOMAIN, RESIDUES 196-364
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 STAR / References: UniProt: Q9WXF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.79 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7, 30% PEG 6000, 1 M LICL 3% 1,2,3-HEPTANETRIOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→52.5 Å / Num. obs: 52532 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.041→45.933 Å / SU ML: 0.59 / σ(F): 1.35 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 2669 5.1 %
Rwork0.2008 --
obs0.2033 52510 96.68 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.937 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1381 Å20 Å2-3.6243 Å2
2--6.3015 Å20 Å2
3----0.1634 Å2
Refinement stepCycle: LAST / Resolution: 2.041→45.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4945 0 0 449 5394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045060
X-RAY DIFFRACTIONf_angle_d0.736859
X-RAY DIFFRACTIONf_dihedral_angle_d13.1941905
X-RAY DIFFRACTIONf_chiral_restr0.044790
X-RAY DIFFRACTIONf_plane_restr0.003958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.041-2.07810.29851160.25032625X-RAY DIFFRACTION97
2.0781-2.11810.27291440.23472612X-RAY DIFFRACTION98
2.1181-2.16130.33641320.22352681X-RAY DIFFRACTION98
2.1613-2.20830.25191240.19882660X-RAY DIFFRACTION98
2.2083-2.25970.24921310.192608X-RAY DIFFRACTION99
2.2597-2.31620.24591580.18692707X-RAY DIFFRACTION98
2.3162-2.37880.25181350.19382598X-RAY DIFFRACTION98
2.3788-2.44880.25231500.18972620X-RAY DIFFRACTION97
2.4488-2.52780.2571450.19332620X-RAY DIFFRACTION98
2.5278-2.61820.21951180.20382654X-RAY DIFFRACTION97
2.6182-2.7230.28781690.20992626X-RAY DIFFRACTION98
2.723-2.84690.30271340.22722618X-RAY DIFFRACTION97
2.8469-2.9970.32391440.23272578X-RAY DIFFRACTION96
2.997-3.18470.26771540.22522654X-RAY DIFFRACTION97
3.1847-3.43050.26821320.21572604X-RAY DIFFRACTION96
3.4305-3.77560.22471590.19062587X-RAY DIFFRACTION96
3.7756-4.32160.1971450.17072605X-RAY DIFFRACTION95
4.3216-5.44340.2211380.17422582X-RAY DIFFRACTION94
5.4434-45.94490.23721410.19912602X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5128-1.0085-1.62630.55570.55961.390.1212-0.0690.3-0.039-0.0116-0.1697-0.04560.0993-0.10410.1834-0.01840.01090.18630.00510.179933.2624-4.566747.3662
25.3516-2.0556-0.63341.22670.55570.51670.0522-0.09850.7317-0.0920.0618-0.27640.02310.0533-0.09910.17360.00790.00430.1084-0.00310.1749-4.803512.972959.7475
32.70720.4757-2.13290.96180.28512.7952-0.0923-0.3845-0.12690.00110.0334-0.11010.17380.41340.07940.20470.0108-0.01930.23540.02320.151747.61-13.270344.5913
42.67630.79831.66430.570.44071.2110.08510.0265-0.20350.0749-0.0059-0.09840.06940.0937-0.06640.14750.0466-0.02670.1006-0.01030.137869.717628.1118.2207
54.51331.79360.28051.35010.30240.6826-0.15960.144-0.58090.06570.1651-0.28170.03180.0275-0.00370.17220.0045-0.00760.0753-0.00290.165831.698310.67796.0689
62.17820.1771.84931.60010.572.5356-0.05640.29720.0212-00.055-0.1688-0.13070.44020.01110.13580.00090.00950.22590.01660.161484.312136.820321.0119
72.65971.3583-1.22020.853-0.57940.95020.0854-0.15580.15030.0256-0.06750.0899-0.02330.0125-0.03230.15610.00620.01810.1185-0.00460.1319-7.53570.189519.8472
84.89091.8638-0.24471.8112-0.0490.46120.07550.05050.48710.0339-0.00480.19890.08320.021-0.06710.1577-0.007-0.01930.06690.00260.153934.173622.29456.3746
92.35610.9326-1.48621.6575-1.22741.53260.1425-0.05160.03720.1245-0.07740.02220.0538-0.039-0.05840.1745-0.00830.00360.2314-0.02830.139-18.518-5.722720.1829
102.1959-1.15541.38510.7604-0.58471.41920.0715-0.0657-0.13220.0441-0.01330.0770.068-0.0873-0.06170.1829-0.0252-0.04020.1071-0.01160.1121-43.997423.490645.6609
114.0468-1.0951.2451.4964-0.27471.23330.09530.1553-0.5295-0.15960.04350.2226-0.0610.1652-0.14380.20670.031-0.01230.1217-0.02540.1762-2.14971.206359.36
122.8657-0.41461.42131.2284-0.59641.1151-0.1541-0.25120.11220.10940.1081-0.014-0.0839-0.20520.06120.18310.0005-0.01390.2795-0.03060.0945-54.841329.184845.5555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:257)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 258:312)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 313:358)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 0:257)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 258:312)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 313:358)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 0:257)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 258:303)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 304:358)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 0:257)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 258:303)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 304:357)

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