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- PDB-4c30: Crystal structure of Deinococcus radiodurans UvrD in complex with... -

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Basic information

Entry
Database: PDB / ID: 4c30
TitleCrystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2
Components
  • DNA HELICASE II
  • DNA STRAND FOR25
  • DNA STRAND 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 / chromatin extrusion motor 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 / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA 3'-5' helicase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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_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_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
F: DNA HELICASE II
I: DNA HELICASE II
K: DNA STRAND FOR25
L: DNA STRAND REV25
X: DNA STRAND FOR25
Y: DNA STRAND REV25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,14816
Polymers326,9908
Non-polymers1,1588
Water1,74797
1
A: DNA HELICASE II
D: DNA HELICASE II
X: DNA STRAND FOR25
Y: DNA STRAND REV25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0748
Polymers163,4954
Non-polymers5794
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-76.3 kcal/mol
Surface area62020 Å2
MethodPISA
2
F: DNA HELICASE II
I: DNA HELICASE II
K: DNA STRAND FOR25
L: DNA STRAND REV25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0748
Polymers163,4954
Non-polymers5794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-70.2 kcal/mol
Surface area62190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.489, 89.785, 293.798
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, -0.00111, -0.001577), (-0.001109, -1, 0.000448), (-0.001577, -0.000447, -1)34.45, 45.44, 146.9
2given(1, 0.000293, 0.00019), (0.000293, -1, 0.000567), (0.00019, -0.5667, -1)34.2, 45.52, 146.9
3given(1, -0.000233, -0.001388), (-0.000233, -1, -0.000208), (-0.001388, 0.000208, -1)34.42, 45.58, 146.9
4given(1, -0.00172, -0.002548), (-0.00172, -1, -4.5E-5), (-0.002548, 5.0E-5, -1)34.55, 45.54, 146.9

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Components

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Protein , 1 types, 4 molecules ADFI

#1: Protein
DNA HELICASE II / UVRD


Mass: 74100.484 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Plasmid: PET151D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9, DNA helicase

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DNA chain , 2 types, 4 molecules KXLY

#2: DNA chain DNA STRAND FOR25


Mass: 7677.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain DNA STRAND REV25


Mass: 7615.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 105 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.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.75 Å3/Da / Density % sol: 60.02 % / Description: NONE
Crystal growDetails: 22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.1 M NA-FLUORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.078
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3→66.2 Å / Num. obs: 62649 / % possible obs: 89 % / Redundancy: 1.5 % / Biso Wilson estimate: 72.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.9 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DRUVRD FORM1

Resolution: 3→66.18 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.889 / SU B: 57.527 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28783 3128 5 %RANDOM
Rwork0.2282 ---
obs0.23114 59507 87.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.631 Å2
Baniso -1Baniso -2Baniso -3
1-7.5 Å20 Å2-0.01 Å2
2---0.6 Å20 Å2
3----6.91 Å2
Refinement stepCycle: LAST / Resolution: 3→66.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20008 1876 68 97 22049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02222463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5442.05930547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.29252530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33623.3691042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.029153475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.16415219
X-RAY DIFFRACTIONr_chiral_restr0.0950.23408
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116688
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
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 241 -
Rwork0.337 4153 -
obs--83.84 %
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)
10.6531-0.00090.06350.4632-1.04514.3406-0.0448-0.0355-0.095-0.0605-0.0247-0.20950.6916-0.52730.06951.1556-0.3-0.03780.8701-0.00790.37547.063-7.095-26.458
20.99060.22010.111.4003-0.04551.86140.0912-0.11360.0847-0.0311-0.18650.04570.13730.01490.09530.73430.00280.02050.86690.0890.598627.76712.681-32.114
30.666-0.1035-0.29540.1452-0.29662.1707-0.1876-0.0129-0.08590.09170.0213-0.18980.0142-0.51870.16631.0130.0301-0.09150.95780.06920.485414.4049.23-13.045
40.5407-0.3813-0.01270.99570.08620.77630.08380.0989-0.12240.1973-0.15790.09640.10740.02390.0740.71870.00290.04460.7969-0.03540.637520.112-0.52662.092
51.84550.24680.00371.76960.57441.4196-0.044-0.01540.11270.0078-0.2211-0.167-0.39570.00190.26510.82170.0753-0.06440.83370.01960.605935.5932.41535.544
61.23190.17891.48492.9742-1.17783.10260.16840.09470.09360.2503-0.11590.38990.08110.0824-0.05250.59640.07510.06390.8504-0.10340.72286.16216.67862.604
70.65370.10290.27520.3754-0.78744.6739-0.11860.02250.0535-0.0337-0.0199-0.2301-0.5615-0.64650.13851.17590.3580.07020.9113-0.01320.3868-28.5251.499171.089
81.2277-0.7399-0.01730.9215-0.10671.63490.05390.1153-0.06820.0952-0.1678-0.1306-0.4813-0.01850.11390.90970.01320.0250.79930.07350.5467-12.5241.632179.943
90.42760.15380.08030.1687-0.25121.7753-0.20990.0172-0.0358-0.09430.0822-0.2143-0.188-0.50790.12770.99340.00810.10731.02120.05350.4914-19.89636.329160.041
100.6120.47440.13291.02480.19230.65560.1038-0.07010.1256-0.1425-0.16250.1016-0.07230.01210.05870.75880.02080.01040.7974-0.03250.6276-14.1746.13584.886
111.30890.02440.26991.66730.33431.485-0.0214-0.0084-0.0958-0.1274-0.1772-0.21880.3969-0.07890.19860.878-0.06810.11360.84180.02330.58541.63443.339111.687
122.11470.0603-1.23742.0062-0.96813.40510.0182-0.2170.0776-0.14070.01290.18550.06620.1743-0.03110.5974-0.05520.01490.8334-0.08950.6893-28.10128.90684.389
130.0627-0.08490.2882.50690.5446.2999-0.09140.17110.00980.1343-0.3917-0.14610.1734-0.44380.48311.01-0.2379-0.06441.05250.12040.2923-15.5934.737127.252
1421.2533-12.0781-7.22726.90924.48615.68830.06012.5762-0.0325-0.1933-1.36440.1874-1.42240.10381.30431.1051-0.034-0.2751.11750.44920.8205-10.58443.954163.052
152.5459-2.0602-1.403512.44232.3620.99510.01180.08560.63061.22040.7745-0.02150.0065-0.2745-0.78631.5204-0.0652-0.23832.00540.58790.8083-7.70336.779145.346
163.58630.21191.77290.555-0.87442.6733-0.2598-0.66320.0173-0.06020.1877-0.08170.0722-0.84540.07211.2483-0.262-0.00630.8235-0.13940.4007-21.35835.989111.912
170.06590.18530.35020.68031.16834.3604-0.0988-0.1816-0.0394-0.1139-0.3084-0.2029-0.0528-0.18620.40720.98670.25620.06461.00640.15840.307218.70210.84719.739
1836.948614.853617.09495.98756.561615.864-0.2934-1.22970.0519-0.0632-0.6461-0.00880.48160.67590.93951.0585-0.05820.11430.8370.2240.392223.7171.632-15.993
193.6356-2.35023.28045.64671.02245.43180.0721-1.6085-0.1051-0.47510.6407-0.31650.0121-1.7037-0.71281.35870.24440.21061.3840.27050.593126.5418.8451.612
203.0364-0.0963-1.33350.6246-0.88792.1832-0.20330.57530.1091-0.07620.0613-0.00850.0229-0.72710.1421.08270.2959-0.0460.8226-0.14050.405312.9379.60335.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 286
2X-RAY DIFFRACTION2A287 - 392
3X-RAY DIFFRACTION3A393 - 661
4X-RAY DIFFRACTION4D7 - 384
5X-RAY DIFFRACTION5D385 - 550
6X-RAY DIFFRACTION6D559 - 662
7X-RAY DIFFRACTION7F7 - 226
8X-RAY DIFFRACTION8F227 - 392
9X-RAY DIFFRACTION9F393 - 661
10X-RAY DIFFRACTION10I7 - 384
11X-RAY DIFFRACTION11I385 - 550
12X-RAY DIFFRACTION12I559 - 662
13X-RAY DIFFRACTION13K1 - 17
14X-RAY DIFFRACTION14K18 - 23
15X-RAY DIFFRACTION15L1 - 7
16X-RAY DIFFRACTION16L8 - 23
17X-RAY DIFFRACTION17X1 - 17
18X-RAY DIFFRACTION18X18 - 23
19X-RAY DIFFRACTION19Y1 - 7
20X-RAY DIFFRACTION20Y8 - 23

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