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- PDB-4c2u: Crystal structure of Deinococcus radiodurans UvrD in complex with... -

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Basic information

Entry
Database: PDB / ID: 4c2u
TitleCrystal structure of Deinococcus radiodurans UvrD in complex with DNA, Form 1
Components
  • DNA HELICASE II
  • FOR25
  • REV25
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA REPAIR / DNA HELICASES / NUCLEOTIDE EXCISION REPAIR
Function / homology
Function and homology information


DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / isomerase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / ATP hydrolysis activity ...DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / isomerase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #160 / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. ...Arc Repressor Mutant, subunit A - #160 / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / NITRATE ION / DNA / DNA (> 10) / DNA 3'-5' helicase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsStelter, M. / Acajjaoui, S. / McSweeney, S. / Timmins, J.
CitationJournal: Plos One / Year: 2013
Title: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd.
Authors: Stelter, M. / Acajjaoui, S. / Mcsweeney, S. / Timmins, J.
History
DepositionAug 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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: DNA HELICASE II
D: DNA HELICASE II
X: REV25
Y: FOR25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,03416
Polymers163,4954
Non-polymers1,53912
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-69 kcal/mol
Surface area62260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.572, 67.448, 386.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 4 - 664 / Label seq-ID: 4 - 664

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DB

NCS oper: (Code: given
Matrix: (-0.001034, -1, 0.00021), (-1, 0.001034, -4.4E-5), (4.4E-5, -0.00021, -1)
Vector: 16.87, 16.81, -96.49)

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA HELICASE II / UVRD


Mass: 74100.484 Da / Num. of mol.: 2 / Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9, DNA helicase

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DNA chain , 2 types, 2 molecules XY

#2: DNA chain REV25


Mass: 7615.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain FOR25


Mass: 7677.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 6 types, 198 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.67 Å3/Da / Density % sol: 58.95 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.0, 0.2 M NA-NITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.55→47.4 Å / Num. obs: 56088 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PJR

3pjr


Resolution: 2.55→47.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / SU B: 20.094 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.619 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26651 2971 5 %RANDOM
Rwork0.21143 ---
obs0.2141 56088 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.55→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 956 94 186 11564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02111847
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7442.07116252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.15451346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85923.291553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.796151831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.04715120
X-RAY DIFFRACTIONr_chiral_restr0.1090.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218867
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 5222 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.220.5
2Dmedium positional0.220.5
1Amedium thermal1.532
2Dmedium thermal1.532
LS refinement shellResolution: 2.547→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 191 -
Rwork0.346 4070 -
obs--98.61 %
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)
10.8464-0.22220.15380.4104-0.03760.3249-0.19830.00620.1299-0.00590.20060.08610.02160.0407-0.00230.18280.0392-0.06850.3531-0.02030.339521.84145.247-83.706
21.08371.5343-0.57664.3465-1.05660.978-0.113-0.2718-0.030.10450.25140.40620.1289-0.3955-0.13840.1580.03670.19540.59650.21840.349-0.1526.387-65.762
32.1414-0.6837-0.84391.3142-0.86431.6533-0.3397-0.68020.4460.2970.2231-0.2698-0.06280.3650.11660.26590.1434-0.12260.4882-0.12160.314431.22451.168-68.9
40.3747-0.20730.00490.8460.11190.31940.20070.01020.1033-0.0303-0.18930.09170.04080.045-0.01150.35210.0419-0.01630.1826-0.05210.3362-26.181-3.211-14.567
55.84362.1498-2.66352.9963-0.16383.30190.72750.14971.0839-0.5348-0.16360.0547-1.0627-0.0948-0.56390.490.07540.22910.07580.15050.4118-11.06619.128-30.868
61.3829-0.4994-1.05282.0315-0.68321.64720.15140.2991-0.2108-0.5748-0.25190.52190.3179-0.11890.10040.46640.1476-0.13140.2557-0.1030.34-34.372-14.318-27.576
713.58370.0257-11.71891.5308-2.18913.8018-0.28270.41410.3302-0.1550.2541-0.4633-0.0597-0.0340.02871.2714-0.33520.28221.38760.10410.957415.37716.094-50.295
80.11150.03030.07650.00840.02060.06240.1920.2976-0.26770.06740.0965-0.06770.09080.1122-0.28863.2192-0.46650.29242.11260.31612.3164-7.666-6.187-43.126
96.1115.01641.34825.72874.71858.3976-0.31170.1363-0.2492-0.44040.3946-0.2111-0.46110.6896-0.08290.59980.11310.01470.5207-0.02270.5264-22.66-9.607-23.225
104.343610.4656-2.826329.3031-12.30739.37971.0874-0.45880.34281.8528-0.42211.0018-0.0547-0.5579-0.66541.157-0.06540.43551.28210.39271.0323-0.6620.692-45.996
110.2401-0.4222-0.1420.80270.2710.09180.114-0.13010.59890.24870.1741-1.04840.08610.007-0.28811.7323-0.42850.23352.4250.48281.816323.02524.462-53.387
1217.20163.890214.55650.98593.021915.62550.4802-0.445-0.46170.2495-0.08950.05230.6247-0.3535-0.39070.5660.07830.03340.58320.03170.566126.5339.486-73.274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 391
2X-RAY DIFFRACTION2A392 - 535
3X-RAY DIFFRACTION3A536 - 664
4X-RAY DIFFRACTION4D4 - 434
5X-RAY DIFFRACTION5D435 - 535
6X-RAY DIFFRACTION6D536 - 664
7X-RAY DIFFRACTION7Y2 - 11
8X-RAY DIFFRACTION8Y12 - 20
9X-RAY DIFFRACTION9Y21 - 24
10X-RAY DIFFRACTION10X1 - 11
11X-RAY DIFFRACTION11X12 - 20
12X-RAY DIFFRACTION12X21 - 24

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