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- PDB-7p8p: Crystal structure of Fhit covalently bound to a nucleotide -

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Basic information

Entry
Database: PDB / ID: 7p8p
TitleCrystal structure of Fhit covalently bound to a nucleotide
ComponentsBis(5'-adenosyl)-triphosphatase
KeywordsHYDROLASE / Fhit / Ap3A
Function / homology
Function and homology information


adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / adenylylsulfatase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity ...adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / adenylylsulfatase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / fibrillar center / nucleotide binding / ubiquitin protein ligase binding / mitochondrion / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / FHIT family / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
Chem-6BI / Bis(5'-adenosyl)-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsHerzog, D. / Missun, M. / Diederichs, K. / Marx, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)MA2288/19 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3 A Elucidates Its Inhibitory Action on Translation.
Authors: Herzog, D. / Jansen, J. / Missun, M. / Diederichs, K. / Stengel, F. / Marx, A.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bis(5'-adenosyl)-triphosphatase
B: Bis(5'-adenosyl)-triphosphatase
C: Bis(5'-adenosyl)-triphosphatase
D: Bis(5'-adenosyl)-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,50012
Polymers75,2174
Non-polymers2,2838
Water1,40578
1
A: Bis(5'-adenosyl)-triphosphatase
D: Bis(5'-adenosyl)-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6775
Polymers37,6092
Non-polymers1,0693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-20 kcal/mol
Surface area12610 Å2
MethodPISA
2
B: Bis(5'-adenosyl)-triphosphatase
C: Bis(5'-adenosyl)-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8227
Polymers37,6092
Non-polymers1,2145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-29 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.422, 61.736, 198.009
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 95 or (resid 96...
d_2ens_1(chain "B" and (resid 2 through 95 or (resid 96...
d_3ens_1(chain "C" and resid 2 through 147)
d_4ens_1(chain "D" and (resid 2 through 95 or (resid 96...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERGLNA1 - 127
d_21ens_1SERHISC1 - 107
d_22ens_1SERGLNC127 - 146
d_31ens_1SERGLNE1 - 127
d_41ens_1SERHISH1 - 107
d_42ens_1SERGLNH120 - 139

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Components

#1: Protein
Bis(5'-adenosyl)-triphosphatase / AP3A hydrolase / AP3Aase / Diadenosine 5' / 5'''-P1 / P3-triphosphate hydrolase / ...AP3A hydrolase / AP3Aase / Diadenosine 5' / 5'''-P1 / P3-triphosphate hydrolase / Dinucleosidetriphosphatase / Fragile histidine triad protein


Mass: 18804.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FHIT / Production host: Escherichia coli (E. coli)
References: UniProt: P49789, bis(5'-adenosyl)-triphosphatase
#2: Chemical
ChemComp-6BI / [(2~{R},3~{S},4~{R},5~{R})-5-[6-(ethylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 522.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28ClN6O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus condition G8: 0.1 M Carboxylic acids, 0.1 M Buffer System 2, 37.5 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999871 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999871 Å / Relative weight: 1
ReflectionResolution: 2.336→46.33 Å / Num. obs: 45307 / % possible obs: 86 % / Redundancy: 5.69 % / Biso Wilson estimate: 39.19 Å2 / CC1/2: 0.989 / Rrim(I) all: 0.218 / Net I/σ(I): 6.93
Reflection shellResolution: 2.336→2.348 Å / Num. unique obs: 3173 / CC1/2: 0.317 / Rrim(I) all: 1.622

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIT

4fit


Resolution: 2.34→46.33 Å / SU ML: 0.3344 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 1979 7.93 %
Rwork0.1928 22991 -
obs0.197 24970 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.32 Å2
Refinement stepCycle: LAST / Resolution: 2.34→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 127 78 4547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064586
X-RAY DIFFRACTIONf_angle_d0.88146218
X-RAY DIFFRACTIONf_chiral_restr0.0507677
X-RAY DIFFRACTIONf_plane_restr0.0076850
X-RAY DIFFRACTIONf_dihedral_angle_d14.21881736
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.964253984895
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.968598125155
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.01320757196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.4283390.4551518X-RAY DIFFRACTION27.98
2.4-2.460.40981000.36611152X-RAY DIFFRACTION63.94
2.46-2.530.37991190.30461370X-RAY DIFFRACTION75.28
2.53-2.620.32111290.28041495X-RAY DIFFRACTION82.39
2.62-2.710.3241450.26921676X-RAY DIFFRACTION92.62
2.71-2.820.32231570.24951822X-RAY DIFFRACTION99.9
2.82-2.950.30221570.23641828X-RAY DIFFRACTION100
2.95-3.10.2591600.21941844X-RAY DIFFRACTION100
3.1-3.290.25351570.20141824X-RAY DIFFRACTION99.9
3.29-3.550.22251580.17671836X-RAY DIFFRACTION100
3.55-3.910.22261590.16091845X-RAY DIFFRACTION100
3.91-4.470.20621630.14391887X-RAY DIFFRACTION99.95
4.47-5.630.19881640.14351891X-RAY DIFFRACTION100
5.63-46.330.21611720.18052003X-RAY DIFFRACTION99.91
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)
17.09963208123-0.4014289459031.103910666858.38409926076-6.157301628687.29777489048-0.321106021622-0.851476453655-0.2875190559020.125703998524-0.2128819082220.04846100165470.2493990342192.017850968260.5239967257930.4816067884170.06923920878190.1382156250380.539454331855-0.009744620900150.302520693799-11.428573685525.447194550524.8784307916
21.3119986885-1.86427719591-0.8283759081492.533396024071.8567910639.963726970280.07754308007050.04750633821310.101644430866-0.223230246412-0.0959026005769-0.1280872637790.2251967559940.2756322199830.005093549759330.619710087375-0.1252855670260.04684970779670.3346251477580.02971765097670.26691655764-14.818547764335.195598853222.4716821027
36.273284054411.319920916624.950883054140.7906270789290.9307159395344.658776594080.1360462240880.0792177801144-0.4598933811-0.216239338153-0.0667455988421-0.1379763833451.064295157690.104757386783-0.3028591167010.607582533847-0.1141081150410.02525364800140.318263333992-0.06790887759010.233406908386-21.837183327528.107220473625.955719077
44.744972736660.520858871592.965295366621.484288609421.162179736996.89626390951-0.201560844567-0.07240763660060.0903729953560.16021958110.0675000363051-0.0468866764172-0.3187295107390.1304252167630.1503966460350.579245483486-0.07313583946850.01817119886920.284526418262-0.04471984561660.23007544593-25.083902281438.286972103127.1132678056
53.348503330360.756796330171-2.04524314546.00419153512-6.332893839178.21688379914-0.3118129408970.384813102746-0.19355672432-0.0371097806330.305752049830.3456633212451.37792662782-0.279354839393-0.07588675398670.605741948361-0.01729418633370.07152172301730.379615320342-0.04700996456070.27939809539-27.296914778223.97283750835.8964149703
66.44774905006-2.096785464923.819358620673.97757922592-1.217184930364.732326035350.43479766320.505539575571-0.131471356337-0.561354208666-0.2226961047740.1718353452430.5169516441350.377247885467-0.2589085669210.511455783731-0.05456493726680.0003008447354420.421832936993-0.03808046352180.218372280606-25.357194963727.62421120727.9589088228
72.017475718-1.45375902681-2.798879927170.7107950428180.1450575624642.88174948218-0.4510774109870.249180624283-2.43822053708-0.51724623945-0.005131165242760.6376093568631.08008894665-0.9382167663280.02029044499720.468309187958-0.337058461012-0.1748744054380.807385153131-0.1150576833470.591609977474-32.919113810324.825091256315.440645671
84.40547024911-5.27853510265-5.552661966736.300361927336.678358042587.401672255940.0930148724647-0.281539027585-0.02088224373450.008713041666490.100084081803-0.0875966057761-0.4413618131990.758271483946-0.1219301506270.44346420491-0.0362423665609-0.04233006260140.428970110901-0.01708087733680.228942706703-18.717260574434.501038567712.16908913
96.645920368-0.8809521995763.160084192453.93032814067-2.096860372629.505417513440.433373697414-0.06003915487110.6483817047560.137621009958-0.08502532557690.395762916362-1.465958985781.07618923633-0.5032594917390.7250469681190.04130734994560.1991346408840.467860424567-0.05434485487880.335272042944-6.4249903109117.244067338226.7861411395
102.54092011737-0.5050330494451.799175712998.526077644266.273215231916.57442091513-0.260637844539-0.4144296207430.0292098788675-0.01137340127570.1273612916250.391348557007-0.1079611648480.2620933300910.1465617976470.6422997802670.03662445813260.05759870620540.4138724145420.02199767212560.285918340385-2.983821794699.3754784741734.096842757
115.887855283484.5699641383-5.164474976265.75494595097-4.684142746874.72545773861.00065630831-1.141738665890.1969307030661.18545624592-0.690489474763-0.244860843972-0.05729575386260.000877982006121-0.4429501264110.507796090538-0.106718733177-0.03957531164170.381807581136-0.1332514248350.3911886936221.44531822329.2005413453328.4908062262
126.841426622883.28705833372-7.119500770393.84950893542-3.143542246988.99637807824-0.03085361188020.7738074392670.0982621817715-0.07708717478560.37334954023-0.00496068143338-0.368790892705-0.927922963996-0.2267556564580.4781649227960.00375151762254-0.01657041965020.254848367086-0.04151070766310.238760921981-4.047003245068.1492433902520.7185161991
137.694080972291.83636175887-6.972796239370.83956661128-2.584380183398.59318625981-0.202191037639-0.3773105101530.2464790780730.01741036575190.1938554939110.05864002187650.2895645845390.02826833751830.1125603852650.4427207631690.00807630045411-0.05581664836620.30996082826-0.06811429278070.201532023662.836635962470.19367386784926.53629561
141.90782339046-2.513560926521.697705346064.95734318176-1.592375482594.679194658380.07761381412080.0165983201711-0.07484827565320.3427594972380.3387488696850.4167010221850.580732446402-0.441588505045-0.2714716829210.349877440493-0.06280448454110.05844150847480.281409135856-0.03715746677640.229291690587-6.96356644653-1.4163383617219.6800907411
153.470777025561.081006770630.9693357272052.580763753971.48876111123.84132860339-0.220687311108-0.04893323066870.0041853703990.129216478547-0.1466776438850.187130460553-0.138395672622-0.561273134160.4083682750440.368996624334-0.0460369068430.03975613397110.384789877583-0.07029783049080.196058020592-7.419593143564.8802144687719.5698898808
160.322226808636-0.878840232768-0.6034491467562.960372719982.17811883141.71781407609-0.458436517212-0.0544311717628-0.57594239012-1.10987185739-0.196586420921.83043216638-0.628062650818-0.9088226128930.309617778760.743525713018-0.0435206470479-0.090350243550.7131268811960.1052639489930.773501132525-18.3623393295-2.1094210395426.1620759673
173.14855217817-4.501469192271.120341340436.73595549556-1.175655104199.03053929450.160199484116-0.699184033626-0.305626048074-0.1435786540270.09906099736650.2073271562130.410060328493-0.247461107037-0.2486292997870.676706956409-0.1016662033490.05046831700480.457824398334-0.01646190731670.286155582107-7.35162147984.4146633221738.0093992002
185.592949134864.42582126763-4.523530378175.20712729663-5.057616740074.94735082983-0.0693148971338-0.975326903416-0.849404139790.9528101303460.1872714897920.02735526483780.3484087958050.02469113043030.2391094515280.7548175508770.251055341982-0.08235312425980.4634538063980.02874908173520.4051451767838.91404960222-18.64159851158.04563473315
193.182271879891.891975655441.93767500222.47108289841.141667433241.30527745163-0.26450272282-0.405292364894-0.623635430054-0.3597625372790.552295637869-0.58964245850.04207024455780.693026188495-0.114696777970.354247439070.04837335736350.008855454722160.487176035095-0.01634894160390.2497987123410.9609289039-8.504844349025.96427068919
202.885400671770.5430251433320.4191026326873.099634338691.332557320834.85708693710.160294481492-0.100105909826-0.1501517651980.175409139515-0.0641043908775-0.1500128501310.5247791116350.132817080435-0.07942511348180.3096442935750.00731491019913-0.01274738567690.259872237485-0.02917560845570.1568520203413.44971456537-4.0960685545810.8117435339
217.780257064351.63598322501-3.934550206370.630197868369-0.2992521735353.82734009161-0.348976276762-0.00668227478134-0.7682634830880.364424274506-0.148969603839-0.2616588827560.793153060708-0.3505308866810.3961244996840.672704463182-0.1185165273220.009752541788590.307745114586-0.0691496267640.341671576896-2.65777431578-13.436539766217.7493606823
229.75707948593-4.426063461553.663265335418.32125147169-5.052741129474.78749864301-0.009947816022951.0050393756-0.334508592775-0.2348949342260.1966171518320.519201033307-0.1405665761080.178134495817-0.05220378285290.3844126172660.0733584691987-0.01750632091050.37680292655-0.1673504954220.248772501871-9.220626878-0.664411243715.99128999595
236.041588100110.263652477069-0.04457096373026.337096829724.987059650763.94479476641-0.3992467037-0.416719508666-0.01225052451110.258767837207-0.09408695097131.41774472291-0.551977092337-0.2219634444680.4557788604870.611234792941-0.05448238872110.0275991591610.497973529267-0.1070842677710.398328662785-13.3523035431-5.6598028859710.8039141129
240.570781020796-0.686440825729-1.123812335761.068970854321.564159621492.38562484006-0.1013534275180.2296521552850.00234856336530.573941341922-0.07237799965850.1703081054950.754563237795-0.7714350133580.2418504842810.704254694057-0.1323399304660.003593482431510.403420324064-0.05287186512210.407759202959-7.38710255367-18.26570272372.95459600167
255.67227472250.686659525352-1.476640936217.095627584761.897376779434.199357858420.116867432914-0.0750374257156-0.0957142260158-0.421736877493-0.0892439045521-0.261236722869-0.272005674404-0.397087509267-0.006863190384970.4902748033050.001182207477960.006348414775570.397122311996-0.02910835767040.1576162293287.16397525362-6.50733156726-4.02700121615
263.265175326250.134260982351-0.9107044393972.59014454356-0.6712419218676.09173546491-0.0767232904713-0.09323649509030.286263217817-0.02768247467790.2129770462150.225349860655-0.688544511037-0.560546086292-0.1320056079690.4972228279860.02605972912780.0184818220360.3265085810760.001395711159310.245573121341-36.105266673139.085314571938.5898842393
273.54241698253-2.14617080808-3.722583472023.226148222583.809366542167.10910471523-0.07914809902930.720840240972-0.458119656662-0.0715914959209-0.5122253328430.4801363872040.0475129271215-1.001842502360.5209924654610.5949605666140.0328971649379-0.01454984998560.5524175357730.01059808189870.362917085679-40.949983947929.106992517142.2213501451
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 11 )AA2 - 111 - 10
22chain 'A' and (resid 12 through 26 )AA12 - 2611 - 25
33chain 'A' and (resid 27 through 46 )AA27 - 4626 - 45
44chain 'A' and (resid 47 through 81 )AA47 - 8146 - 80
55chain 'A' and (resid 82 through 88 )AA82 - 8881 - 87
66chain 'A' and (resid 89 through 102 )AA89 - 10288 - 101
77chain 'A' and (resid 103 through 131 )AA103 - 131102 - 111
88chain 'A' and (resid 132 through 147 )AA132 - 147112 - 127
99chain 'C' and (resid 2 through 11 )CE2 - 111 - 10
1010chain 'C' and (resid 12 through 18 )CE12 - 1811 - 17
1111chain 'C' and (resid 19 through 26 )CE19 - 2618 - 25
1212chain 'C' and (resid 27 through 51 )CE27 - 5126 - 50
1313chain 'C' and (resid 52 through 72 )CE52 - 7251 - 71
1414chain 'C' and (resid 73 through 88 )CE73 - 8872 - 87
1515chain 'C' and (resid 89 through 102 )CE89 - 10288 - 101
1616chain 'C' and (resid 103 through 131 )CE103 - 131102 - 111
1717chain 'C' and (resid 132 through 147 )CE132 - 147112 - 127
1818chain 'B' and (resid 2 through 11 )BC2 - 111 - 10
1919chain 'B' and (resid 12 through 26 )BC12 - 2611 - 25
2020chain 'B' and (resid 27 through 81 )BC27 - 8126 - 80
2121chain 'B' and (resid 82 through 95 )BC82 - 9581 - 94
2222chain 'B' and (resid 96 through 109 )BC96 - 10995 - 108
2323chain 'B' and (resid 110 through 119 )BC110 - 119109 - 118
2424chain 'B' and (resid 120 through 131 )BC120 - 131119 - 130
2525chain 'B' and (resid 132 through 147 )BC132 - 147131 - 146
2626chain 'D' and (resid 2 through 102 )DH2 - 1021 - 101
2727chain 'D' and (resid 103 through 147 )DH103 - 147102 - 139

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