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- PDB-4c2t: Crystal structure of full length Deinococcus radiodurans UvrD in ... -

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Basic information

Entry
Database: PDB / ID: 4c2t
TitleCrystal structure of full length Deinococcus radiodurans UvrD in complex with DNA
Components
  • DNA HELICASE II
  • DNA STRAND FOR28
  • DNA STRAND REV28
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 / DNA / DNA (> 10) / DNA 3'-5' helicase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.997 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 1.1May 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
B: DNA HELICASE II
C: DNA HELICASE II
D: DNA HELICASE II
M: DNA STRAND FOR28
N: DNA STRAND REV28
O: DNA STRAND REV28
P: DNA STRAND FOR28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,24816
Polymers365,1268
Non-polymers2,1228
Water00
1
A: DNA HELICASE II
B: DNA HELICASE II
M: DNA STRAND FOR28
N: DNA STRAND REV28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,6248
Polymers182,5634
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-59.6 kcal/mol
Surface area62890 Å2
MethodPISA
2
C: DNA HELICASE II
D: DNA HELICASE II
O: DNA STRAND REV28
P: DNA STRAND FOR28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,6248
Polymers182,5634
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-56.8 kcal/mol
Surface area63230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.457, 390.044, 71.559
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA HELICASE II / UVRD


Mass: 82707.492 Da / Num. of mol.: 4
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
#2: DNA chain DNA STRAND FOR28


Mass: 8569.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain DNA STRAND REV28


Mass: 8578.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.61 Å3/Da / Density % sol: 57.91 % / Description: NONE
Crystal growDetails: 16-22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 6.5-7.5, 0.1-0.3 M NA-NITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 4→46.1 Å / Num. obs: 30051 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 149.79 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 4→4.22 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIFFERENT CRYSTAL FORM OF DRUVRD

Resolution: 3.997→46.147 Å / SU ML: 0.53 / σ(F): 0 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 1516 5 %
Rwork0.2464 --
obs0.2477 30051 94.51 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 167.099 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 207.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.0222 Å20 Å223.0968 Å2
2---32.4405 Å20 Å2
3---20.4183 Å2
Refinement stepCycle: LAST / Resolution: 3.997→46.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20337 2080 128 0 22545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623161
X-RAY DIFFRACTIONf_angle_d1.07531771
X-RAY DIFFRACTIONf_dihedral_angle_d18.9058786
X-RAY DIFFRACTIONf_chiral_restr0.0793507
X-RAY DIFFRACTIONf_plane_restr0.0053824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9971-4.1260.41421290.4062183X-RAY DIFFRACTION80
4.126-4.27340.43091200.36212368X-RAY DIFFRACTION86
4.2734-4.44440.35981370.31062513X-RAY DIFFRACTION92
4.4444-4.64650.3221230.28282554X-RAY DIFFRACTION94
4.6465-4.89120.29561380.27032657X-RAY DIFFRACTION96
4.8912-5.19720.25241550.25072685X-RAY DIFFRACTION97
5.1972-5.59790.31321400.272658X-RAY DIFFRACTION98
5.5979-6.16010.35751550.28982697X-RAY DIFFRACTION99
6.1601-7.04870.30541430.26332750X-RAY DIFFRACTION99
7.0487-8.87030.19711440.20322750X-RAY DIFFRACTION100
8.8703-46.15050.19241320.18172720X-RAY DIFFRACTION99
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)
14.5842.0173-0.78541.1259-2.70314.63350.17741.5638-0.6118-0.8991-0.20180.67880.456-0.745-02.23350.1290.12421.7976-0.22571.9337-52.5174-103.2967-8.4292
25.138-1.82041.71322.9589-2.27033.95410.758-0.1073-0.620.1591-0.3308-1.06170.12220.433402.1425-0.407-0.05311.91260.20351.8287-21.8042-111.98253.5837
33.23692.5952-2.34886.3045-1.93291.29590.4232-0.35510.40070.2953-0.28770.1981-0.3574-0.036601.8754-0.1174-0.14271.7914-0.10581.3239-50.1672-107.99245.6969
41.07070.79550.81522.52780.84483.0596-0.2840.4971-1.1676-0.87190.32020.1520.09890.5626-01.9499-0.0208-0.02961.85980.05231.6334-51.084-132.67992.1255
50.8352-1.33320.8220.8807-0.60241.60020.1703-0.39780.53030.1534-0.3274-1.30080.3870.153202.3460.139-0.00572.3091-0.18172.2988-18.8226-126.0395-12.9791
62.7281.32130.41792.45611.17321.2406-0.421.2477-1.065-0.34090.22950.4046-0.07610.191403.09840.11430.09942.6878-0.39472.044-31.1526-128.2686-19.9352
76.60670.75970.72666.3747-1.25521.52460.1152-0.7644-0.32690.6986-0.1995-0.28330.07080.301201.6377-0.20680.00291.86840.10961.1144-51.7355-124.953915.5171
83.1555-0.5320.54152.04251.10224.5113-0.04970.6408-0.363-0.8218-0.43380.7336-0.9289-1.3039-01.81130.11740.10981.71550.02692.26095.9362-181.0939-48.0217
91.6549-0.4143-0.37312.84760.5596.05840.50030.0715-0.21380.7704-0.652-0.10380.0208-0.063-01.6904-0.1117-0.11711.69370.15642.15719.7061-178.3495-21.8466
100.05090.8023-0.76224.9734-0.24812.1206-0.31990.055-0.9724-0.192-0.2288-0.28830.78490.237601.65820.0903-0.13341.85790.0631.960818.7595-185.2543-46.4351
113.6987-0.14971.08823.96230.03340.91320.312-0.1850.3465-0.64090.1960.3257-0.8802-0.097301.6628-0.0863-0.07561.6780.18771.756122.9086-153.7694-51.5357
121.0708-2.53812.73690.04020.211.82790.1064-0.7029-0.2690.6173-0.21370.5550.26110.0974-02.07270.0630.00212.49830.16432.59-8.2634-161.6817-21.483
130.6141-1.1675-0.32452.3036-1.70854.4624-0.18520.39330.453-0.47440.3119-0.2296-0.4854-1.4341-01.94560.3598-0.37372.9022-0.15242.7895-10.7621-158.6886-35.8961
143.00272.0561-0.90048.1788-1.9684.3343-0.20950.1818-0.17110.5634-0.0969-1.1223-0.5510.370401.1628-0.0382-0.16491.88010.14911.498929.2814-161.9491-45.4532
153.8178-1.0013-0.54264.2550.77164.3109-0.0865-2.1151.35011.1551-0.46721.2076-0.1138-0.933802.2559-0.32270.07672.2739-0.25611.8635-17.2106-87.752732.6687
164.91961.09180.1761.6392-0.20461.32380.6076-0.22861.22030.1576-0.2599-0.6018-0.31590.664702.0350.09430.20282.00660.01992.340613.7807-79.111220.4329
174.3346-0.30781.00883.6386-0.99162.17360.3106-0.12250.3136-0.2979-0.32110.17230.1187-0.081402.0071-0.1873-0.0081.8857-0.07121.6984-14.6394-83.609918.0942
180.48690.3846-0.30840.4718-0.66532.32720.1112-0.8320.82861.2225-0.34940.3516-0.90050.154-02.717-0.2210.19281.9922-0.36423.1445-16.3021-58.945420.5083
190.85441.70830.5110.15740.22170.02510.2679-0.2642-0.69440.3394-0.203-0.5133-0.03020.378802.72-0.49220.04222.705-0.46892.655316.5849-65.162637.1011
202.37411.7615-4.36581.8993-1.5703-0.15670.2147-0.44780.52411.4551-0.62630.2859-0.250.1452-03.6253-0.2278-0.08192.611-0.42432.60136.0895-62.571143.5881
213.828-0.17160.99883.1569-1.97922.48010.08010.43830.9744-0.2478-0.09560.925-0.6236-0.1275-02.38460.0358-0.03721.91410.0292.4042-16.3654-66.83328.8785
222.87341.54230.57152.80992.15081.3376-0.4834-0.06520.28880.392-0.51711.05911.4252-1.532202.0084-0.0185-0.08772.2373-0.32362.360117.9177-6.603671.2232
231.5039-0.3673-1.31341.63961.66334.513-0.36670.6479-0.5874-0.58120.0308-0.58290.41650.019102.053-0.07580.28681.92530.07792.1337.5398-10.655350.484
241.8829-0.9620.73814.23050.03644.152-0.07030.0492-0.09740.6799-0.51690.12240.4533-0.0799-01.87340.1023-0.08451.9569-0.02422.103929.992-8.356277.5994
252.9261-1.21451.82371.3853-0.2470.34450.37950.4294-0.77110.1698-0.194611.3423-0.7849-02.7551-0.21670.05622.0262-0.36842.772327.1854-33.041278.4814
26-0.0325-0.03340.1637-0.05431.36090.35090.2186-0.181-0.066-1.2190.0886-1.3781-0.14370.54302.8065-0.28180.16112.7644-0.35312.707321.0154-27.508242.692
271.1848-3.3113-1.57682.58620.93231.94010.04060.29620.0819-0.0272-0.62381.30670.3133-0.6815-02.4487-0.4478-0.10352.9188-0.43443.04711.8095-29.37450.5563
282.3458-0.20320.76573.95530.36834.6187-0.7082-0.7935-0.840.6650.2509-0.08361.13570.056502.4690.1409-0.09191.92420.10812.244339.4992-24.811882.2335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:113)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 114:194)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 195:348)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 349:391)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 392:440)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 454:555)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 562:662)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 7:132)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 133:208)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 209:317)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 318:388)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 389:453)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 454:552)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 562:662)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 7:113)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 114:194)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 195:348)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 349:391)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 392:442)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 443:551)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 552:662)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 7:133)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 134:194)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 195:348)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 349:391)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 392:440)
27X-RAY DIFFRACTION27(CHAIN D AND RESID 441:555)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 562:661)

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