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- PDB-6p4o: Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaer... -

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Basic information

Entry
Database: PDB / ID: 6p4o
TitleComplex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution
Components
  • DNA-dependent ATPase XPBII
  • Endonuclease Bax1
KeywordsHYDROLASE/DNA BINDING PROTEIN / Helicase / nuclease / HYDROLASE / HYDROLASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


DNA 3'-5' helicase / transcription preinitiation complex / 3'-5' DNA helicase activity / transcription initiation at RNA polymerase II promoter / endonuclease activity / Hydrolases; Acting on ester bonds / hydrolase activity / DNA binding / ATP binding / metal ion 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
Endonuclease Bax1 / DNA 3'-5' translocase XPB2
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsFan, L. / DuPrez, K.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GMK8893 United States
CitationJournal: To Be Published
Title: Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution
Authors: Fan, L. / 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
E: DNA-dependent ATPase XPBII
F: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,44514
Polymers336,0226
Non-polymers4248
Water1,00956
1
A: DNA-dependent ATPase XPBII
B: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2687
Polymers112,0072
Non-polymers2615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area48980 Å2
MethodPISA
2
C: DNA-dependent ATPase XPBII
D: Endonuclease Bax1


Theoretical massNumber of molelcules
Total (without water)112,0072
Polymers112,0072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-18 kcal/mol
Surface area48270 Å2
MethodPISA
3
E: DNA-dependent ATPase XPBII
F: Endonuclease Bax1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1705
Polymers112,0072
Non-polymers1633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-36 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.723, 125.851, 148.970
Angle α, β, γ (deg.)90.000, 101.520, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTYRTYRAA-2 - 43118 - 451
21GLYGLYTYRTYRCC-2 - 43118 - 451
12SERSERSERSERAA-1 - 43419 - 454
22SERSERSERSEREE-1 - 43419 - 454
13METMETLYSLYSBB1 - 47621 - 496
23METMETLYSLYSDD1 - 47621 - 496
14METMETLYSLYSBB1 - 47821 - 498
24METMETLYSLYSFF1 - 47821 - 498
15SERSERTYRTYRCC-1 - 43119 - 451
25SERSERTYRTYREE-1 - 43119 - 451
16METMETLYSLYSDD1 - 47621 - 496
26METMETLYSLYSFF1 - 47621 - 496

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein DNA-dependent ATPase XPBII


Mass: 52887.230 Da / Num. of mol.: 3
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: pET15b / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q970I2
#2: Protein Endonuclease Bax1


Mass: 59120.078 Da / Num. of mol.: 3
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 , 4 types, 64 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.11 Å3/Da / Density % sol: 60.42 % / Description: Hexagonal plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-Cl, pH 8.0, 50 mM Sodium Carbonate, 32% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2015
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→145.969 Å / Num. obs: 57984 / % possible obs: 85 % / Redundancy: 4.5 % / Rpim(I) all: 0.072 / Rrim(I) all: 0.161 / Rsym value: 0.144 / Net I/av σ(I): 4 / Net I/σ(I): 6.6 / Num. measured all: 258254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.15-3.323.70.7051.12906578610.3970.8140.7051.779.5
3.32-3.5240.4551.63022775370.2460.520.4552.880.4
3.52-3.764.30.3472.13099271910.180.3930.3473.781.4
3.76-4.074.60.2532.83135468190.1260.2840.2535.182.5
4.07-4.454.90.1783.83100763400.0850.1980.1787.783.9
4.45-4.984.90.1454.82932459430.0690.1610.1459.786.3
4.98-5.754.80.1424.72633955030.0670.1580.1428.990.5
5.75-7.044.50.1275.22155948240.0630.1430.1279.194
7.04-9.964.50.0767.31755338610.0380.0850.07613.797.2
9.96-29.9145.10.078.21083421050.0330.0780.0717.194.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.97 Å29.91 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.8.3phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Coot0.8.8model building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TNU

5tnu


Resolution: 3.15→29.93 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.569 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 1999 3.5 %RANDOM
Rwork0.2651 ---
obs0.2657 55900 84.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 291.81 Å2 / Biso mean: 78.856 Å2 / Biso min: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20.09 Å2
2---1.02 Å20 Å2
3---2 Å2
Refinement stepCycle: final / Resolution: 3.15→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19961 0 21 56 20038
Biso mean--65.72 53.21 -
Num. residues----2753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01220357
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.63327700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.652747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25322.01811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.232152997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.271595
X-RAY DIFFRACTIONr_chiral_restr0.0630.22866
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215399
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A11412
12C11412
21A11503
22E11503
31B10870
32D10870
41B10767
42F10767
51C11434
52E11434
61D10744
62F10744
LS refinement shellResolution: 3.15→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 136 -
Rwork0.407 3789 -
all-3925 -
obs--78.97 %

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