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- PDB-2va8: DNA Repair Helicase Hel308 -

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Basic information

Entry
Database: PDB / ID: 2va8
TitleDNA Repair Helicase Hel308
ComponentsSKI2-TYPE HELICASE
KeywordsHYDROLASE / HEL308 / SSO2462 / HELICASE / DNA REPAIR / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJohnson, K.A. / Richards, J. / Liu, H. / McMahon, S. / Oke, M. / Carter, L. / Naismith, J.H. / White, M.F.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the DNA Repair Helicase Hel308 Reveals DNA Binding and Autoinhibitory Domains.
Authors: Richards, J.D. / Johnson, K.A. / Liu, H. / Mcrobbie, A.M. / Mcmahon, S. / Oke, M. / Carter, L. / Naismith, J.H. / White, M.F.
History
DepositionAug 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 31, 2014Group: Data collection / Derived calculations
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SKI2-TYPE HELICASE
B: SKI2-TYPE HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8429
Polymers163,1692
Non-polymers6727
Water2,630146
1
A: SKI2-TYPE HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7773
Polymers81,5851
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SKI2-TYPE HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0656
Polymers81,5851
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.657, 138.083, 107.551
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.44, -0.581, -0.685), (-0.574, -0.769, 0.283), (-0.691, 0.269, -0.671)
Vector: 0.27901, 0.12339, 0.154)

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Components

#1: Protein SKI2-TYPE HELICASE / SSO2462


Mass: 81584.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: PBL 2025 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE FOR THE PROTEIN HAS BEEN DEPOSITED WITH THE EMBL DATABASE WITH ACCESSION NUMBER: ...THE SEQUENCE FOR THE PROTEIN HAS BEEN DEPOSITED WITH THE EMBL DATABASE WITH ACCESSION NUMBER: AM778123. AT THE TIME OF PROCESSING, NO UNIPROT SEQUENCE ACCESSION IS AVAILABLE. AT A LATER DATE WHEN AN UNIPROT DATABASE REFERENCE IS AVAILABLE, THE CROSS-REFERENCE AND MAPPING WILL BE MAINTAINED VIA THE MSD SIFTS INITIATIVE AS DESCRIBED IN THE WWPDB ANNOTATION POLICY. HTTP://WWW.EBI.AC.UK/MSD-SRV/DOCS/SIFTS/ AUTHOR'S NOTE: THOUGH WE CLONED THE ENTIRE SEQUENCE, OUR COLLABORATOR NOW BELIEVES THAT THE TRUE START OF THE PROTEIN IS METHIONINE 8, HENCE OUR STRUCTURE IS NUMBERED FROM THIS RESIDUE.

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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: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 15.3% PEG8000, 0.1M SODIUM CACODYLATE, PH6.5, 0.13M AMMONIUM SULFATE AND 0.03M MAGNESIUM CHLORIDE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF BM1420.934
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDDec 12, 2006MIRRORS
ADSC CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMOND (111)SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 79222 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRACED FROM MAD DATASET

Resolution: 2.3→107.21 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.656 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3995 5 %RANDOM
Rwork0.212 ---
obs0.214 75297 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-3.11 Å2
2---0.11 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 35 146 11297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.98715325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49751384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87924.651516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02152142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4461572
X-RAY DIFFRACTIONr_chiral_restr0.0760.21736
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028342
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.25157
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.27782
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5051.57143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.827211128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34134807
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1014.54197
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 294
Rwork0.228 5486
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)
12.6615-1.24671.59283.2545-0.81534.79470.0463-0.1744-0.20680.1622-0.0185-0.01330.2487-0.0465-0.0277-0.26750.0250.0642-0.05860.0631-0.253114.626812.28451.9516
24.1083-1.39130.13876.6701-0.02652.77590.1713-0.5127-0.7936-0.05960.04370.43650.7429-0.3747-0.215-0.0838-0.1853-0.00030.01740.2373-0.1392-12.5622-0.202341.5706
32.7158-1.44490.24693.3009-0.32371.4391-0.19740.67860.2756-0.2422-0.0019-0.41940.13190.73430.1993-0.2381-0.01880.12220.29730.1591-0.127921.862624.446328.6527
45.05611.83570.90163.4581-0.2733.2191-0.35250.0360.4727-0.3106-0.09670.1669-0.42360.02210.4492-0.2356-0.0053-0.0301-0.30020.0245-0.1995-4.347134.05227.7923
56.03340.16261.28317.48616.607514.5522-0.0397-0.4812-0.27461.1688-0.26930.55010.3939-0.45660.3090.23830.11080.1009-0.1438-0.18940.1422-12.292145.598853.9844
62.7163-0.64871.30593.1174-1.61924.95390.2440.57970.0931-0.4614-0.16530.0441-0.13060.522-0.0787-0.03710.087-0.02-0.0925-0.0308-0.1937-20.510313.9322-25.0592
75.91731.76340.17544.6271-0.32244.6713-0.57340.18850.7843-0.43770.0675-0.0484-1.03250.4240.50590.1257-0.0781-0.2283-0.36580.0649-0.0302-18.239835.9494-2.8769
83.1607-0.6522-1.40383.4725-0.65562.76320.32160.3111-0.2094-0.1034-0.011-0.37510.54130.7179-0.31060.05440.2628-0.2288-0.1042-0.189-0.0018-8.5349-6.3344-11.3002
93.3633-0.62821.05374.44891.13213.73390.3659-0.5126-0.55680.34360.06630.17710.5516-0.2741-0.4323-0.1951-0.0899-0.018-0.28940.1166-0.1522-24.77371.033110.1609
1014.79332.51218.54713.3354.269711.63810.5703-0.7783-0.3058-0.6-0.70250.995-0.3956-1.30980.1322-0.18970.04340.00510.1613-0.06870.2791-51.82555.51490.8589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 199
2X-RAY DIFFRACTION2A200 - 415
3X-RAY DIFFRACTION3A416 - 500
4X-RAY DIFFRACTION4A501 - 644
5X-RAY DIFFRACTION5A645 - 705
6X-RAY DIFFRACTION6B1 - 199
7X-RAY DIFFRACTION7B200 - 415
8X-RAY DIFFRACTION8B416 - 500
9X-RAY DIFFRACTION9B501 - 644
10X-RAY DIFFRACTION10B645 - 705

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