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- PDB-5lkm: RadA bound to dTDP -

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Basic information

Entry
Database: PDB / ID: 5lkm
TitleRadA bound to dTDP
ComponentsDNA repair protein RadA
KeywordsDNA BINDING PROTEIN / Helicase / recombination / DNA-binding protein / Lon-protease
Function / homology
Function and homology information


recombinational repair / ATP-dependent DNA damage sensor activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
DNA repair protein RadA / Subunit ChlI of Mg-chelatase / AAA domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / DNA repair protein RadA / DNA repair protein RadA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRapisarda, C. / Remaut, H. / Fornzes, R.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council France
CitationJournal: Nat Commun / Year: 2017
Title: Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension.
Authors: Marie, L. / Rapisarda, C. / Morales, V. / Berge, M. / Perry, T. / Soulet, A.L. / Gruget, C. / Remaut, H. / Fronzes, R. / Polard, P.
History
DepositionJul 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn / struct_keywords / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _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

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RadA
B: DNA repair protein RadA
C: DNA repair protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5239
Polymers148,2443
Non-polymers1,2796
Water0
1
A: DNA repair protein RadA
B: DNA repair protein RadA
C: DNA repair protein RadA
hetero molecules

A: DNA repair protein RadA
B: DNA repair protein RadA
C: DNA repair protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,04718
Polymers296,4886
Non-polymers2,55912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area27070 Å2
ΔGint-156 kcal/mol
Surface area89200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.400, 169.900, 187.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPHEPHEAA54 - 45254 - 452
21THRTHRPHEPHEBB54 - 45254 - 452
12ASNASNVALVALAA66 - 45166 - 451
22ASNASNVALVALCC66 - 45166 - 451
13ASNASNPHEPHEBB68 - 45268 - 452
23ASNASNPHEPHECC68 - 45268 - 452

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA repair protein RadA /


Mass: 49414.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R800 / Gene: radA, ERS022181_02072
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0T7K9X0, UniProt: Q8DRP0*PLUS
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 200 mM MgF 100 mM HEPES pH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→49.21 Å / Num. obs: 20413 / % possible obs: 100 % / Redundancy: 66.5 % / Rmerge(I) obs: 0.1837 / Rrim(I) all: 0.1852 / Net I/σ(I): 22.76
Reflection shellRmerge(I) obs: 1.071 / Rrim(I) all: 1.079

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lko

5lko
PDB Unreleased entry


Resolution: 3.5→49.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.945 / SU B: 51.177 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22398 1022 5 %RANDOM
Rwork0.1829 ---
obs0.18497 19401 99.94 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 147.869 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.92 Å2
Refinement stepCycle: 1 / Resolution: 3.5→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8530 0 78 0 8608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198703
X-RAY DIFFRACTIONr_bond_other_d0.0070.028704
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.99211757
X-RAY DIFFRACTIONr_angle_other_deg1.594319988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53351094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39424.669362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.196151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6051561
X-RAY DIFFRACTIONr_chiral_restr0.0950.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029664
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021839
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_it6.51511.5264421
X-RAY DIFFRACTIONr_mcbond_other6.51511.5274420
X-RAY DIFFRACTIONr_mcangle_it10.26617.295500
X-RAY DIFFRACTIONr_mcangle_other10.26517.2895501
X-RAY DIFFRACTIONr_scbond_it7.04712.3954282
X-RAY DIFFRACTIONr_scbond_other7.04112.3944274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.51118.3496245
X-RAY DIFFRACTIONr_long_range_B_refined18.82234633
X-RAY DIFFRACTIONr_long_range_B_other18.82134618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A404380.12
12B404380.12
21A441940.13
22C441940.13
31B397340.12
32C397340.12
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 75 -
Rwork0.198 1415 -
obs--100 %
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)
16.9596-2.72613.27441.1019-1.26511.5654-0.40510.38871.0706-0.008-0.1217-0.487-0.30470.09610.52681.00290.15070.25040.8805-0.2530.5357-45.9754-131.2515-67.8487
21.761-1.56370.94332.5191-1.14532.6816-0.21730.05790.2269-0.18360.59880.0839-0.10040.0609-0.38150.2516-0.2604-0.0020.40840.10060.2928-26.5275-110.1337-57.4117
32.5816-0.2821-0.14540.96681.19672.95740.00050.1649-0.22360.1207-0.00470.11740.05950.02980.00420.18730.06860.10380.06040.00830.0947-40.6919-113.1855-22.7127
40.5874-1.6052-0.72954.98312.18570.9770.25970.24680.3002-0.98520.1006-0.9588-0.4725-0.0609-0.36030.8375-0.16220.07351.1330.00780.9194-10.5913-104.5332-67.6952
52.88660.81281.13034.661-0.13060.58220.6071.09070.2740.7329-0.86980.29480.31270.53330.26280.38730.05880.33110.72870.02090.3561-16.565-75.8482-59.1504
62.01660.1512-0.87352.88761.46982.5211-0.1350.1122-0.20040.00910.2905-0.367-0.0948-0.0194-0.15540.041-0.00460.03990.1342-0.00780.1649-20.6189-91.5163-22.7177
70000000000000000.2132000.213200.2132000
82.58682.54380.7492.83880.98223.3871-0.32920.3885-0.4899-0.04770.2651-0.334-0.1101-0.43520.06410.2735-0.09430.180.4040.0280.2787-40.1203-50.2867-57.8832
91.8816-0.8076-0.79392.0556-0.51812.8447-0.14040.13810.10020.0302-0.0692-0.3215-0.1217-0.00980.20960.1134-0.1064-0.0860.13470.0960.1209-29.7096-63.1999-23.1452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 64
2X-RAY DIFFRACTION2A65 - 274
3X-RAY DIFFRACTION3A275 - 452
4X-RAY DIFFRACTION4B54 - 63
5X-RAY DIFFRACTION5B68 - 274
6X-RAY DIFFRACTION6B275 - 452
7X-RAY DIFFRACTION7C56 - 64
8X-RAY DIFFRACTION8C66 - 274
9X-RAY DIFFRACTION9C275 - 452

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