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- PDB-5tnu: S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5tnu
TitleS. tokodaii XPB II crystal structure at 3.0 Angstrom resolution
ComponentsDNA-dependent ATPase XPBII
KeywordsTRANSCRIPTION / Helicase / NER
Function / homology
Function and homology information


hydrolase activity / DNA binding / ATP binding
Similarity search - Function
Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal ...Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-dependent ATPase XPBII
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsDuPrez, K.T. / Hilario, E. / Wang, I. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108893 United States
CitationJournal: Anal.Chem. / Year: 2018
Title: Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA.
Authors: Kahanda, D. / DuPrez, K.T. / Hilario, E. / McWilliams, M.A. / Wohlgamuth, C.H. / Fan, L. / Slinker, J.D.
History
DepositionOct 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: DNA-dependent ATPase XPBII
B: DNA-dependent ATPase XPBII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82028
Polymers105,7742
Non-polymers2,04626
Water2,324129
1
A: DNA-dependent ATPase XPBII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,29019
Polymers52,8871
Non-polymers1,40218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-dependent ATPase XPBII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5319
Polymers52,8871
Non-polymers6438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.922, 160.922, 122.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: -1 - 422 / Label seq-ID: 19 - 442

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

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Components

#1: Protein DNA-dependent ATPase XPBII


Mass: 52887.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: xpb2, ST1613, STK_16130 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 pLysS Rosetta / References: UniProt: Q970I2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1:1 ratio of protein with 10 mM sodium citrate pH 5.6, 1770 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→29.88 Å / Num. obs: 31341 / % possible obs: 99.9 % / Redundancy: 23.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.374 / Rpim(I) all: 0.078 / Rrim(I) all: 0.382 / Net I/σ(I): 11.2 / Num. measured all: 740378 / Scaling rejects: 440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.05-3.2123.42.90410524445040.6290.6092.9672100
9.64-29.8822.90.0652470310800.9990.0140.06633.896.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.33 Å29.88 Å
Translation8.33 Å29.88 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31287
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
12.34-10051.80.313504
9.84-12.3446.50.658507
8.45-9.8441.20.708564
7.53-8.4540.80.697645
6.85-7.5339.70.71709
6.33-6.85380.686755
5.91-6.3332.80.721829
5.57-5.91310.737859
5.27-5.5726.50.772910
5.03-5.2723.90.811964
4.81-5.0320.30.852983
4.62-4.8119.40.8641040
4.45-4.6217.70.8551070
4.29-4.4517.90.8761119
4.16-4.2916.60.8871162
4.03-4.1618.90.8521176
3.92-4.0319.90.8321219
3.81-3.9219.90.8381255
3.71-3.8117.70.8571283
3.62-3.7121.10.8451312
3.54-3.6218.40.8511337
3.46-3.5419.30.8471378
3.39-3.4621.40.8261405
3.32-3.3922.20.8141434
3.25-3.3222.40.8051456
3.19-3.2523.10.7821484
3.13-3.1922.60.7791523
3.05-3.1331.30.6682405

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLM7.2.0data reduction
Aimless0.5.12data scaling
PHASER2.5.7phasing
DM6.5.013phasing
PDB_EXTRACT3.15data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FWR

2fwr


Resolution: 3.05→29.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.1998 / WRfactor Rwork: 0.1745 / FOM work R set: 0.7979 / SU B: 17.044 / SU ML: 0.292 / SU R Cruickshank DPI: 0.8848 / SU Rfree: 0.3317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.885 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1562 5 %RANDOM
Rwork0.1961 ---
obs0.1976 29713 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 328.86 Å2 / Biso mean: 90.199 Å2 / Biso min: 19.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2--2.1 Å20 Å2
3----4.2 Å2
Refinement stepCycle: final / Resolution: 3.05→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 109 129 6636
Biso mean--97.32 61.5 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196606
X-RAY DIFFRACTIONr_bond_other_d0.0020.026095
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9928947
X-RAY DIFFRACTIONr_angle_other_deg0.817314031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3555850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61723.699246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3181534
X-RAY DIFFRACTIONr_chiral_restr0.0740.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027307
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021323
Refine LS restraints NCS

Ens-ID: 1 / Number: 20024 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.05→3.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 111 -
Rwork0.346 2130 -
all-2241 -
obs--99.96 %

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