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- PDB-7ujb: N-terminal domain deletion variant of Eta -

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Basic information

Entry
Database: PDB / ID: 7ujb
TitleN-terminal domain deletion variant of Eta
ComponentsDEAD/DEAH box RNA helicase
KeywordsTRANSCRIPTION / TERMINATION
Function / homology
Function and homology information


catalytic activity, acting on DNA / DNA geometric change / helicase activity / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
Protein of unknown function DUF5814 / Family of unknown function (DUF5814) / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 ...Protein of unknown function DUF5814 / Family of unknown function (DUF5814) / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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
DEAD/DEAH box RNA helicase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.12 Å
AuthorsQayyum, M.Z. / Murakami, K.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087350 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex.
Authors: Marshall, C.J. / Qayyum, M.Z. / Walker, J.E. / Murakami, K.S. / Santangelo, T.J.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
SupersessionDec 20, 2023ID: 7SMO
Revision 1.1Dec 20, 2023Group: Advisory / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_database_PDB_obs_spr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEAD/DEAH box RNA helicase
B: DEAD/DEAH box RNA helicase
C: DEAD/DEAH box RNA helicase
D: DEAD/DEAH box RNA helicase


Theoretical massNumber of molelcules
Total (without water)289,3924
Polymers289,3924
Non-polymers00
Water00
1
A: DEAD/DEAH box RNA helicase


Theoretical massNumber of molelcules
Total (without water)72,3481
Polymers72,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DEAD/DEAH box RNA helicase


Theoretical massNumber of molelcules
Total (without water)72,3481
Polymers72,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DEAD/DEAH box RNA helicase


Theoretical massNumber of molelcules
Total (without water)72,3481
Polymers72,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DEAD/DEAH box RNA helicase


Theoretical massNumber of molelcules
Total (without water)72,3481
Polymers72,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.242, 135.242, 262.353
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1(chain "C" and resid 196 through 828)
d_4ens_1(chain "D" and resid 196 through 828)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALGLYA1 - 633
d_21ens_1VALGLYB1 - 633
d_31ens_1VALGLYC4 - 636
d_41ens_1VALGLYD4 - 636

NCS oper:
IDCodeMatrixVector
1given(-0.999995900096, 0.0028517067636, -0.000259922591042), (-0.0028514017285, -0.999995254414, -0.00116647249526), (-0.000263247795062, -0.00116572656911, 0.999999285891)135.08656081, 156.434396278, 0.107102533646
2given(-0.500260092918, 0.865868089222, 0.00350592357629), (0.865872699661, 0.500264260244, -0.000371353304432), (-0.0020754312405, 0.00284991027323, -0.999993785279)67.5914376369, 39.0939723681, 34.8594829488
3given(0.497050642924, -0.867719488064, -0.00188372011634), (-0.867721527423, -0.497049228492, -0.00118966457571), (9.5993506083E-5, 0.00222586803881, -0.999997518145)135.646117183, 234.232848757, 34.7095325405

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Components

#1: Protein
DEAD/DEAH box RNA helicase


Mass: 72347.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0566 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5JF65

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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: 4.79 Å3/Da / Density % sol: 74.3 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.0, 4.5 M NaCl, 3% ethylene glycol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 4.1→43.48 Å / Num. obs: 41317 / % possible obs: 99.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 177.31 Å2 / CC1/2: 0.993 / Net I/σ(I): 13.2
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.41 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 4.12→43.48 Å / SU ML: 0.8161 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 43.5925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.303 1822 4.87 %
Rwork0.2502 35576 -
obs0.2528 37398 90.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 242.97 Å2
Refinement stepCycle: LAST / Resolution: 4.12→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20234 0 0 0 20234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620590
X-RAY DIFFRACTIONf_angle_d0.949527753
X-RAY DIFFRACTIONf_chiral_restr0.04983130
X-RAY DIFFRACTIONf_plane_restr0.0063561
X-RAY DIFFRACTIONf_dihedral_angle_d15.44847929
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.751354636593
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.760466702986
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.886015010267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.12-4.230.40681150.38082199X-RAY DIFFRACTION71.35
4.23-4.350.42651190.3492330X-RAY DIFFRACTION77.13
4.35-4.490.42331340.32652489X-RAY DIFFRACTION82.72
4.49-4.650.30561300.30312670X-RAY DIFFRACTION87.47
4.65-4.840.34631390.2972776X-RAY DIFFRACTION90.19
4.84-5.060.37971430.29412674X-RAY DIFFRACTION90.23
5.06-5.330.31561440.33922803X-RAY DIFFRACTION91.35
5.33-5.660.4411500.34132837X-RAY DIFFRACTION93.31
5.66-6.090.30871480.34362884X-RAY DIFFRACTION94.99
6.1-6.70.38991470.31022952X-RAY DIFFRACTION97.09
6.71-7.670.3431510.27672984X-RAY DIFFRACTION98.4
7.67-9.640.19591500.18253039X-RAY DIFFRACTION99.1
9.65-43.480.24451520.16252939X-RAY DIFFRACTION97.05
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)
16.91589103536-1.47568612171-0.1537759151078.58728739582-3.828437428376.901101939410.03309370101021.21694886692-0.575093572414-1.84008842551-0.0950497259501-0.3824643582240.5688582505760.320562562432-0.1024388584612.01745460412-0.1528881081280.5096463478541.48437999186-0.4073443105521.3839798078283.430368852664.07249798396.82738587444
29.82042519574.504729729162.279827457568.48732471767-3.145338019960.513234856541-0.190351104867-1.07880174031-0.119499540005-1.628627635080.0673344917486-0.8003376085840.297057167271-0.5940559130380.04834055793152.26747431257-0.3197395339750.1632835571261.743313715930.2757805933731.4354130919287.27449130689.410756530222.3006690452
35.81440282969-4.7685656432-0.442859272153.407585745220.540636425390.952265813713-0.654906915090.155397073641-1.477372781180.65613650839-1.08525249483-1.246654233391.554173820190.1442642605351.244261049773.26025103974-0.0525409334830.5041077745041.9509873937-0.3275373580722.78920413949100.58964281348.29876075618.2872297454
45.561179647513.484879936090.7137192565347.127243691274.982258600627.4696088866-0.3241989448610.0059891311668-1.93722936720.3579116058990.496259985584-1.240681171460.6409302545110.614193721188-0.1597903735821.719501368780.2804857981620.1872543366481.25933055350.4382513770011.6382828406188.866307147165.799693317944.2287069989
56.13639776738-1.62478506208-0.6506416413757.181902492733.744537396327.397261951860.3226002824830.8973433561930.862639846108-1.13913492917-0.07084535025650.958531535467-0.619587449837-0.538043512752-0.3489303275291.97741345368-0.244656829614-0.5821165538681.297123620030.4141761865281.0736037296151.816975990292.13462055786.82905768066
69.419413082932.83962708669-3.660638349427.690340989042.363640757161.194887727320.163811524879-0.9780996871590.63745671408-1.45013643863-0.04672547083051.17104531371-0.5199199447990.783922398262-0.291514586642.23468418877-0.311321753976-0.1947044309181.63538088474-0.3301164670361.4974594714248.084853009466.739672262122.2959223112
78.215176839841.888879445224.356004142969.88694561069-2.47846568637-0.5133926266011.1432711548-0.757721855304-0.156577341944-0.602836071344-1.183460219551.412280964490.933271618863-0.874572673739-0.08418693855871.88992513117-0.389223928137-0.1380828057341.73273069921-0.2537454858551.95216038045101.308875677159.33378583712.6413992299
83.830662500680.06460070760830.1231602252829.578538349890.5220388446150.1831148559380.445430577598-1.00837617870.0769175198449-0.142197047499-0.504486843642-1.84099850863-1.025103778861.112142216660.0207481376352.10101592014-0.3391133805810.1189773848971.560161586680.2087668328051.84649196383101.4569982114.08009609812.6425299891
95.803866461330.3919540784183.529463391742.863206325681.471125008242.34792379149-0.438486815068-1.328341074840.03131157646181.67451225678-0.06282495670970.08746335571610.155430071704-0.3648427383620.1924534837271.93079849064-0.3644952719280.6228371785581.91694098731-0.4040246258831.3784303287381.4587520072143.41023824628.0300590683
104.936646264980.46946583636-1.685767868963.29366206026-0.4046880131695.538792605310.183312080526-1.909612249110.07720635168781.158413157310.162983133076-0.1178108163770.3498952452690.46917430282-0.4972549764392.19796990274-0.46176202638-0.5619625825141.954005269090.2677138765051.71104263137121.439319338129.91926041627.9938581121
117.0578493432-3.331709407033.179734585473.577446497291.146010064815.2161238529-0.9998466356011.39452388741.85299828444-1.44306949914-0.478417684792-0.644879640066-2.267640969880.0587651624271.033589333342.785136102290.0588457054579-0.1444296131671.99632456190.626931659042.7366005774234.6744982752107.77859047118.2447542299
122.242119934271.32606016649-0.484974163613.125629644964.108520301191.1161071425-1.124167436140.790185578981-0.9410387920970.554779044461-0.01194025604723.758628019150.803431622018-2.287595712380.743932823012.64071455414-0.4210751661520.8217760067542.91680484557-0.102816424493.836352817659.1633376203150.35603106516.4925776839
133.52713160239-1.362230184742.397351921442.72160242358-2.841004492534.6586893852-1.788470242931.59424690147-1.601346064160.09406228670790.0386540434835-3.36208947904-3.425526172912.05869262710.8038520953213.04539809463-0.845057995937-0.8720106045222.831271327590.01113956295183.41625390604143.722832599122.91142377916.5753897405
143.388953072683.03817367784-1.633308665899.26988893777-4.366538911425.8302329854-0.7585713115360.01830790933091.693477544010.2334263775550.5941259146120.626261618729-0.974896808653-0.6077013002430.08643343340281.434265596970.261921868695-0.09102725092761.44001550666-0.4890173379941.4321110630346.376494996990.346567400644.258676678
159.174980144514.86619551506-3.717728288939.35694906204-4.534350326118.05694731758-0.1110225680020.974282803149-1.408702844860.8405499553750.2209944727861.22314556748-0.577311655697-1.799026214630.08057338042061.514818737680.0908678749705-0.2709907801811.8485182118-0.5146526786761.5198409483680.2639673554148.953480932-9.36124374602
167.963207470816.88034182932.55570374323.442422126382.810007678116.783256406950.3615422816750.3073245048192.648381416061.54506557012-0.0927828207958-1.502991838121.041515759981.503219148810.3142173032911.612703822520.0548917287130.3093865015631.659853784980.6534493592371.468971824122.644804369124.394810099-9.3664190789
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 196 through 400 )AA196 - 4001 - 205
22chain 'A' and (resid 401 through 574)AA401 - 574206 - 379
33chain 'A' and (resid 575 through 652 )AA575 - 652380 - 457
44chain 'A' and (resid 653 through 828 )AA653 - 828458 - 633
55chain 'B' and (resid 196 through 400 )BB196 - 4001 - 205
66chain 'B' and (resid 401 through 574)BB401 - 574206 - 379
77chain 'C' and (resid 401 through 574)CC401 - 574209 - 382
88chain 'D' and (resid 401 through 574)DD401 - 574209 - 382
99chain 'C' and (resid 196 through 400 )CC196 - 4004 - 208
1010chain 'D' and (resid 196 through 400 )DD196 - 4004 - 208
1111chain 'B' and (resid 575 through 652 )BB575 - 652380 - 457
1212chain 'C' and (resid 575 through 652 )CC575 - 652383 - 460
1313chain 'D' and (resid 575 through 652 )DD575 - 652383 - 460
1414chain 'B' and (resid 653 through 828 )BB653 - 828458 - 633
1515chain 'C' and (resid 653 through 828 )CC653 - 828461 - 636
1616chain 'D' and (resid 653 through 828 )DD653 - 828461 - 636

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