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- PDB-6p4w: XPB helicase in a complex with truncated Bax1 from Sulfurisphaera... -

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Basic information

Entry
Database: PDB / ID: 6p4w
TitleXPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution
Components
  • DNA-dependent ATPase XPBII
  • Endonuclease Bax1
KeywordsHYDROLASE/DNA BINDING PROTEIN / Helicase / endonuclease / HYDROLASE / HYDROLASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


endonuclease activity / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
Protein of unknown function DUF790, endonuclease-like / Protein of unknown function (DUF790) / 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. ...Protein of unknown function DUF790, endonuclease-like / Protein of unknown function (DUF790) / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Endonuclease Bax1 / DNA-dependent ATPase XPBII
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.956 Å
AuthorsFan, L. / He, F. / DuPrez, K.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108893 United States
CitationJournal: To Be Published
Title: XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution
Authors: Fan, L. / He, F. / DuPrez, K.T.
History
DepositionMay 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: DNA-dependent ATPase XPBII
B: Endonuclease Bax1
C: DNA-dependent ATPase XPBII
D: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,38928
Polymers190,3284
Non-polymers1,06124
Water1,72996
1
A: DNA-dependent ATPase XPBII
B: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,73015
Polymers95,1642
Non-polymers56613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-127 kcal/mol
Surface area39140 Å2
MethodPISA
2
C: DNA-dependent ATPase XPBII
D: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65913
Polymers95,1642
Non-polymers49511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-111 kcal/mol
Surface area39470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.415, 101.369, 114.476
Angle α, β, γ (deg.)83.090, 81.150, 90.170
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA0 - 4341 - 435
21SERSERCC0 - 4341 - 435
12GLUGLUBB1 - 3722 - 373
22GLUGLUDD1 - 3722 - 373

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein DNA-dependent ATPase XPBII


Mass: 50728.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: xpb2, ST1613, STK_16130 / Plasmid: pET28a / Details (production host): Precision protease site / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q970I2
#2: Protein Endonuclease Bax1


Mass: 44435.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: bax1, ST1614, STK_16140 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q970I1

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Non-polymers , 5 types, 120 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.4 Å3/Da / Density % sol: 63.85 % / Description: Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM Ammonium citrate, pH 7.5, 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2018
RadiationMonochromator: Single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 51223 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Χ2: 0.577 / Net I/σ(I): 5.8 / Num. measured all: 179503
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-33.30.82225230.6320.5290.9820.43698.3
3-3.063.50.725760.680.4380.8290.45498.7
3.06-3.113.60.53425580.780.3320.6310.46498.5
3.11-3.183.50.44125110.840.2750.5220.44698.5
3.18-3.253.40.38625400.8580.2470.460.46298.7
3.25-3.323.50.32226090.9010.2020.3820.48798.8
3.32-3.413.60.25225080.9350.1530.2960.50898.7
3.41-3.53.60.20126190.9570.1230.2360.53499
3.5-3.63.60.17225160.9620.1070.2030.58699.1
3.6-3.723.50.14125670.9760.0870.1660.65199
3.72-3.853.30.11925360.9840.0770.1430.71599
3.85-43.50.10826010.9830.0680.1280.71599.2
4-4.193.50.09125480.9880.0570.1080.73199.3
4.19-4.413.40.0825560.9890.0510.0950.6799.2
4.41-4.683.70.07225870.9920.0440.0850.6899.3
4.68-5.043.60.06925910.9920.0430.0810.67999.3
5.04-5.553.40.07325480.9890.0460.0870.67599.5
5.55-6.353.50.07425870.990.0460.0870.61299.7
6.35-83.60.06325730.9940.0390.0740.64799.7
8-503.50.05325690.9960.0330.0620.36899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.36 Å49.21 Å
Translation6.36 Å49.21 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
Coot0.8.8model building
HKL-2000data reduction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TNU

5tnu


Resolution: 2.956→29.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2513 4.9 %RANDOM
Rwork0.183 ---
obs0.1855 48672 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 237.99 Å2 / Biso mean: 77.683 Å2 / Biso min: 27.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20.03 Å2-0.04 Å2
2--0.15 Å2-0.08 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.956→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12904 0 42 96 13042
Biso mean--98.61 58.92 -
Num. residues----1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01213214
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.63417877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77951619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04322.199632
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.045152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5661576
X-RAY DIFFRACTIONr_chiral_restr0.0740.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029777
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A133760.13
12C133760.13
21B106500.15
22D106500.15
LS refinement shellResolution: 2.956→3.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 184 -
Rwork0.317 3200 -
all-3384 -
obs--89.41 %

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