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- PDB-9jue: Roadblock3 homodimer structure from Candidatus Prometheoarchaeum ... -

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Basic information

Entry
Database: PDB / ID: 9jue
TitleRoadblock3 homodimer structure from Candidatus Prometheoarchaeum syntrophicum strain MK-D1
ComponentsRoadblock/LC7 domain protein
KeywordsUNKNOWN FUNCTION / Roadblock domain homodimer
Function / homologyRoadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Roadblock/LC7 domain protein
Function and homology information
Biological speciesPromethearchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPonlachantra, K. / Robinson, R.C.
Funding support Thailand, United States, 3items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
Simons FoundationGBMF9743 United States
Other privateMoore Foundation GBMF9743 United States
CitationJournal: To Be Published
Title: Roadblock domain protein from Asgard archaea
Authors: Ponlachantra, K. / Robinson, R.C.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Roadblock/LC7 domain protein
C: Roadblock/LC7 domain protein
B: Roadblock/LC7 domain protein
A: Roadblock/LC7 domain protein
F: Roadblock/LC7 domain protein
E: Roadblock/LC7 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5467
Polymers84,3086
Non-polymers2381
Water1,820101
1
D: Roadblock/LC7 domain protein
E: Roadblock/LC7 domain protein


Theoretical massNumber of molelcules
Total (without water)28,1032
Polymers28,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17 kcal/mol
Surface area11450 Å2
MethodPISA
2
C: Roadblock/LC7 domain protein
F: Roadblock/LC7 domain protein


Theoretical massNumber of molelcules
Total (without water)28,1032
Polymers28,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-19 kcal/mol
Surface area11250 Å2
MethodPISA
3
B: Roadblock/LC7 domain protein
A: Roadblock/LC7 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3413
Polymers28,1032
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-17 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.692, 88.909, 112.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Roadblock/LC7 domain protein


Mass: 14051.306 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Promethearchaeum syntrophicum (archaea)
Gene: DSAG12_02037 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9DBI1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 293.15 K / Method: microbatch
Details: 0.2 M sodium chloride 0.1 M HEPES pH 7.0 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→19.86 Å / Num. obs: 35992 / % possible obs: 96.71 % / Redundancy: 5.5 % / Biso Wilson estimate: 42.53 Å2 / CC1/2: 0.978 / CC star: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.057 / Rrim(I) all: 0.141 / Net I/σ(I): 17.71
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1 / Num. unique obs: 3236 / CC1/2: 0.618 / CC star: 0.874 / Rpim(I) all: 0.506 / Rrim(I) all: 0.893 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.86 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1746 4.86 %
Rwork0.2093 34216 -
obs0.211 35962 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 15 101 5500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285515
X-RAY DIFFRACTIONf_angle_d0.53167480
X-RAY DIFFRACTIONf_chiral_restr0.0451966
X-RAY DIFFRACTIONf_plane_restr0.0045925
X-RAY DIFFRACTIONf_dihedral_angle_d13.34762064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.31721310.29442491X-RAY DIFFRACTION86.19
2.26-2.340.28361330.25842771X-RAY DIFFRACTION94.87
2.34-2.420.29571340.24032750X-RAY DIFFRACTION94.71
2.42-2.520.28781500.22842772X-RAY DIFFRACTION96.31
2.52-2.630.29761620.23492826X-RAY DIFFRACTION97.08
2.63-2.770.23851450.22532861X-RAY DIFFRACTION97.79
2.77-2.940.32451480.23322858X-RAY DIFFRACTION98.27
2.94-3.170.26091550.22792899X-RAY DIFFRACTION99.06
3.17-3.490.24111520.20372933X-RAY DIFFRACTION99.45
3.49-3.990.24661350.18732968X-RAY DIFFRACTION99.49
3.99-5.010.20431330.16882998X-RAY DIFFRACTION99.75
5.01-19.860.22721680.22093089X-RAY DIFFRACTION99.06
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)
13.152596751591.716144285290.8024806473093.482073722591.110249436463.429067824780.2330669751420.2793881033380.00239263787817-1.55288771757-0.3437700855060.119558623307-0.813360026668-0.1123555224660.001603282320070.7529540571060.0780698399895-0.1036107939360.445421062885-0.02900318927540.42660914821749.064349027321.77256615284.48684496059
21.067800621310.24680763791.101830117162.172464755471.443369202271.762625666240.3909330245040.00595305995975-0.275501667628-0.110243731046-0.2959190825160.06803198210520.401949860818-0.477518516250.0002808916985310.398022184026-0.0254229914852-0.06225432483310.38061817619-0.03392839380660.42840615649150.12897810936.1216974973713.2711072237
31.47156282928-2.247515972640.2883738851274.957873922520.9158737690123.040229860030.17970896172-0.6647213139110.01403349973630.520382269307-0.2071788838320.1706787174290.374468728773-0.1533997367133.68197603753E-50.343098437487-0.0662855109460.01650747200020.476813827987-0.05586653160230.33381038729350.236024296112.600095580719.7674653633
41.34081042548-1.70799598174-1.206067707842.860933221810.7214638975861.672137058580.367192739279-0.701071784475-0.27868839013-0.459632133591-0.445182110167-0.218417547829-0.218993945329-0.328739838887-3.20107556254E-50.389724856736-0.00830017603828-0.04423811474690.474004808337-0.03504915106740.30098360097550.519189336319.300694066213.358880821
50.7342272940460.448352331818-0.904855160081.322019807840.3493765016061.25015685676-0.0374107411677-0.006768739630320.616808847051-0.291021367425-0.6592500842391.12936498893-0.158242966274-0.503300337321-0.00188361678880.5297779260490.0660297872176-0.1827173579120.482687306157-0.1672240101620.53885243654840.906847318522.608493715713.1007662031
60.6395675641360.185654467746-0.3298661935820.6763540748080.2618297717640.7039813147770.215573334446-0.605460008409-1.231035687990.317530995013-0.453626845941.262491927620.254639114457-0.0906229853116-0.0132515514171.3058192948-0.05586116630190.2808837972230.6489493690250.1442246232240.80313950038149.4343499144-27.704263131929.5224884219
70.5749515910420.924432937908-0.1423553072621.51171475693-0.2002194516880.07101738154531.01777558045-0.419424050065-0.7581626476971.23464885296-0.6832250524530.0411155065351-0.3437852150650.4013768197660.05379250895070.5590346921170.151336283529-0.09764514824180.529783690340.1461632815780.56731263150857.9869598767-25.855801420223.7507850567
80.9314385677971.22413372783-0.3636485001784.441446366861.34026529882.06582060633-0.391744874492-0.2226286937760.02965758592152.03973472596-0.0497058896705-0.328125029079-0.287929145111-0.0142922368792-0.01084268310460.6924200022180.070260081030.003647147818470.483259378749-0.02663494323630.44469676606453.2033409229-11.050968175124.9880489343
90.4269286463290.3489280684561.434524912443.663332679040.7512371596143.05100883818-0.1792135444330.233297751974-0.3304476531850.38705153804-0.02790773763210.4179973265830.433766155971-0.359944397836-0.000336290564490.4445329417450.07812451363090.06463005584320.378313572755-0.01959930294350.40442680753452.8585061058-14.513073383816.0386360876
102.930235009422.619255374181.366687888366.24887412091-4.649660524689.67021368708-0.633754714008-0.196189362788-0.6477849811220.03311657722370.356092161674-1.43905849687-0.9516017761691.59123123054-1.457289276160.6306495812280.2755472936790.1383525714250.659748994632-0.1859943420760.96384900184166.020828936-24.846905594514.3543783008
110.657714800817-0.3074077397970.02038357931090.339002311579-0.49406976630.422046251625-0.4792676755850.843866492502-0.5832230228180.4431424010880.2003202716260.7403938399840.509924010711-1.13569868794-0.000222727715050.6324469829090.03639766100440.1915710340020.527604367964-0.05280210424510.76238351273747.1709625898-25.166810745318.7078901201
121.281720579630.7890818826550.1181857524831.85198417458-0.207339799730.874304517495-0.310060902264-0.6606306540530.3263007543451.30692134483-0.154328837592-0.990806486775-0.857820578513-0.592682231154-0.02893034626430.7627393430950.0724300214610.01493910927010.6780580682680.008099784385390.43266874917219.7582089155-1.2839805386535.9244578672
133.704760080630.3021068269312.037472548252.308382581310.3734117279374.767300802610.0249194052006-0.143926268179-0.04900020989740.287486178509-0.3285555714290.503582577061-0.210004237012-0.406896382516-0.01437735165530.3053607746960.1462302641760.07901129613380.422157620004-0.0291282466780.35681351730815.4339378109-7.0925996473127.8901238507
141.17184703352-0.08511266954511.249634420711.12597227806-0.784600348031.4696545319-0.286653357512-0.494100468158-0.3632480911510.0303843681674-0.128554555032-0.1944428593490.4947829888161.111992893770.000138562650940.316866571930.0684280428575-0.009536368144310.4900917180940.04884099812950.42085103842323.0846977724-14.858525370117.1851833933
152.116415067681.69298015837-1.113065773261.17972656371-0.3059514287843.26759807137-0.1688451486680.158362609888-0.2140294677350.0613141285433-0.0146857037598-0.0897590779788-0.2497051291350.579010703428-0.006203969580590.2294576125120.07360812435450.008641875474930.4847937390580.02264642890540.34721374910423.6499111042-6.4540844943216.9884329928
161.961369428490.0638864071241-2.006485887442.172845393380.5389290124722.967193054310.0255838560222-0.2215843342610.7439919553510.1214662580580.0761030173065-0.268793753567-0.836092340170.4517752887660.001321699596420.4849864576690.01001067766850.01774038594810.517927115610.07800441243810.47916769446423.93298381811.2587169938824.7514147019
174.650967154210.5504196067920.8104883268423.8223309936-0.7645464583136.14623775648-0.002291938795310.3381173456530.180058728121-0.545952938384-0.2399530087730.0386541983656-0.2297599734960.430316067345-9.98521997228E-50.349534184559-0.06519280004270.04559603244760.4471204931430.001236667810590.34394341688726.3774964909-5.05366311361-6.83664454151
185.079087917810.0856345112341-2.45041495392.18741942766-1.497372312286.82739715432-0.135164823440.0017661729570.214695297878-0.2173269679190.147428137210.155854665111-0.335007461523-0.125846718978.42146570613E-50.179055287387-0.0426945301604-0.01597298724450.347277486015-0.03948490486050.35430606248419.5686817899-5.954221464163.92655306468
198.644135866651.162585591372.341469138971.78121056019-1.552337393443.033285768361.502518621253.530903851270.162683532488-2.90174835711-0.390003925473-1.67528158535-0.817157065650.4246556520171.238048959871.178760200290.3578706215260.6596892781011.049422788210.1976952440570.6058671046364.9355118377-6.95712930648-9.62375820152
202.50784901265-1.999146699410.06505777253122.71995653658-1.181829433582.063669303280.6666160448040.2035625273810.383867170546-1.01925451732-0.587272278432-0.557641016643-0.200587021991-0.199942235784-0.000120009574630.7002998159280.1521554755590.09330054321090.5115991621420.008707023286220.55906481291157.3739183405-3.45515286407-2.2001207928
210.903923483693-0.493169185763-0.1355209483782.031412945451.790287333321.27631793728-0.400088472468-0.2905721078040.4265711043450.610475260966-0.106661581935-1.02009282419-0.8504534451330.128248022153-0.008947838533330.304555892906-0.0423739076175-0.02366664247130.383942622867-0.07541583802560.59046154929659.7047153021-2.7761817536512.6139563111
221.5888652065-1.883618038160.408910129423.209431940470.8270474893164.126630407280.1101371338690.0341511067424-0.08919655176750.4195234976990.0446873572046-0.3799697302850.03821922261450.3390603146410.0004237639545190.271414066638-0.0397569242942-0.02109966239350.4047532978740.03834353399270.48816581151961.0372569807-10.741838096410.4640924687
231.62512449012-1.69758088299-0.6255213623292.0459234068-0.2891655151151.920609019460.0119730338402-0.3413955945990.142032551815-0.95368643782-0.4016645587951.320727548640.340705693854-0.48270259588-6.47578821103E-50.5230099784520.02385944523120.008103330410540.477698878761-0.05807248021390.5972689628454.6918614142-12.84729613631.24251649032
240.669067661207-0.7029463051371.422068006332.02805968817-2.659573554815.309795824680.9971244085531.769417991880.549463177317-1.89364367736-1.00219870877-1.338592049061.749938026141.267379143170.2881859432880.6570391870250.2782003309850.1961229269160.6045872399440.09149477758330.88955704586967.0335883429-13.5245442153-1.03021333166
250.9993880290780.43512907377-0.2603011511570.875245234462-0.5078070656160.4126625684520.339063071494-1.100478651210.1651261561142.517246135030.548085045932-1.208453475551.13971688868-0.5233984897140.1114295720361.48857724106-0.191452200312-0.54953718040.7311728517310.1276454510620.68960788293259.33501245269.4616238066543.7539565296
261.73738409273-0.397949868391-0.04606310856454.103874930050.4816275967910.2082666532760.8186347596220.0336247737661-0.08529641332362.67424933898-0.9610373710040.2787252102870.1978425065110.685484099622-0.02463742838091.6919430526-0.379990568345-0.06689618417920.3656572137440.008550511362740.44279490053952.771911025110.480809709236.7354202162
271.379694105540.0277017348679-0.2164656258730.0519430585649-0.06093568572441.697309696190.1221824568410.3157023928620.2711580361241.05864634377-0.349303111953-0.8386532569871.49564319981-0.245993050574-0.1341406537031.26645891557-0.00215611860734-0.4556724095480.4401161960580.1220298620420.81026640220960.114910855-0.062564923390334.1674578439
282.53820257346-1.273708572391.919136209234.958604919821.86482966222.845675882120.01737070207630.443506118141-0.4996520991170.7260011258180.246790521766-0.3540129208081.29917800651-0.292825884064-0.00392515954350.6331022204750.0725047244766-0.2230920203990.381611396571-0.06011307979170.49931042421455.51571081592.2560272265325.6149438202
291.845176961631.355373624510.9442149700244.948106644490.6159894773824.139081590160.1608951764810.37138964365-0.1226167645120.429255139644-0.0327042134358-0.6102445960030.5074936607620.1462658267360.0005482096480680.430874502503-0.0541053099882-0.1064011299950.354649903992-0.01400570540750.42312370480857.013429735911.311015284623.2078749141
305.896861445930.512750288832-2.459690093590.8568673275030.7655433701222.258092047461.510144363291.243480188081.081284826671.09883117401-0.4461213125170.5579712896690.0280294668832-1.070631180620.4515387860690.643161323838-0.380230758874-0.5156880528920.447907027896-0.2010489134840.068569998366649.831294837812.508079420131.9104342685
310.94308750884-1.017211795740.5080096557551.30569918327-1.0690799311.535985913750.7832999761680.6969661410190.1580355389650.890597412319-0.960753190249-0.9626399027570.2487693265011.03164240397-0.04990922475760.846153828744-0.136523763906-0.2742630160870.5357970253410.06817451079170.67815144118461.344497812915.942214039434.7035965411
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 12 through 51 )DA12 - 511 - 40
22chain 'D' and (resid 52 through 72 )DA52 - 7241 - 61
33chain 'D' and (resid 73 through 94 )DA73 - 9462 - 83
44chain 'D' and (resid 95 through 110 )DA95 - 11084 - 99
55chain 'D' and (resid 111 through 131 )DA111 - 131100 - 120
66chain 'C' and (resid 11 through 23 )CB11 - 231 - 13
77chain 'C' and (resid 24 through 36 )CB24 - 3614 - 26
88chain 'C' and (resid 37 through 72 )CB37 - 7227 - 62
99chain 'C' and (resid 73 through 105 )CB73 - 10563 - 95
1010chain 'C' and (resid 106 through 110 )CB106 - 11096 - 100
1111chain 'C' and (resid 111 through 130 )CB111 - 130101 - 120
1212chain 'B' and (resid 11 through 24 )BC11 - 241 - 14
1313chain 'B' and (resid 25 through 51 )BC25 - 5115 - 41
1414chain 'B' and (resid 52 through 72 )BC52 - 7242 - 62
1515chain 'B' and (resid 73 through 105 )BC73 - 10563 - 95
1616chain 'B' and (resid 106 through 131 )BC106 - 13196 - 121
1717chain 'A' and (resid 12 through 51 )AD12 - 511 - 40
1818chain 'A' and (resid 52 through 131 )AD52 - 13141 - 120
1919chain 'F' and (resid 11 through 25 )FE11 - 251 - 15
2020chain 'F' and (resid 26 through 51 )FE26 - 5116 - 41
2121chain 'F' and (resid 52 through 72 )FE52 - 7242 - 62
2222chain 'F' and (resid 73 through 98 )FE73 - 9863 - 88
2323chain 'F' and (resid 99 through 110 )FE99 - 11089 - 100
2424chain 'F' and (resid 111 through 129 )FE111 - 129101 - 119
2525chain 'E' and (resid 12 through 24 )EF12 - 241 - 13
2626chain 'E' and (resid 25 through 36 )EF25 - 3614 - 25
2727chain 'E' and (resid 37 through 45 )EF37 - 4526 - 34
2828chain 'E' and (resid 46 through 72 )EF46 - 7235 - 61
2929chain 'E' and (resid 73 through 98 )EF73 - 9862 - 87
3030chain 'E' and (resid 99 through 110 )EF99 - 11088 - 99
3131chain 'E' and (resid 111 through 129 )EF111 - 129100 - 118

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