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Basic information

Entry
Database: PDB / ID: 7bmm
TitleCrystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form
ComponentsPPK2 domain-containing protein
KeywordsTRANSFERASE / Polyphosphate / ATP / kinase
Function / homologyPolyphosphate:nucleotide phosphotransferase, PPK2 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / polyphosphate kinase activity / polyphosphate metabolic process / P-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / Polyphosphate kinase-2-related domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSilva, S.T.N. / Romao, C.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: To Be Published
Title: Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form
Authors: Silva, S.T.N. / Romao, C.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PPK2 domain-containing protein
B: PPK2 domain-containing protein
C: PPK2 domain-containing protein
D: PPK2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,94612
Polymers122,1984
Non-polymers7488
Water8,665481
1
A: PPK2 domain-containing protein
D: PPK2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3845
Polymers61,0992
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-41 kcal/mol
Surface area25320 Å2
MethodPISA
2
B: PPK2 domain-containing protein
C: PPK2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5627
Polymers61,0992
Non-polymers4635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-30 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.925, 78.605, 111.451
Angle α, β, γ (deg.)90.000, 109.207, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
PPK2 domain-containing protein / Polyphosphate kinase 2


Mass: 30549.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Gene: DR_0132 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9RY20, ATP-polyphosphate phosphotransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0,04 M potassium phosphate 2% PEG 8K 8% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.06→83.98 Å / Num. obs: 46075 / % possible obs: 92.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.77 Å2 / CC1/2: 0.987 / Net I/σ(I): 6.3
Reflection shellResolution: 2.06→2.346 Å / Redundancy: 6.8 % / Num. unique obs: 2305 / CC1/2: 0.537 / % possible all: 72.8

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Processing

Software
NameVersionClassification
Coot0.9.3model building
PHENIX1.19_4092refinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6aqe
Resolution: 2.06→83.98 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2146 4.66 %
Rwork0.1942 43909 -
obs0.1967 46055 51.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.71 Å2
Refinement stepCycle: LAST / Resolution: 2.06→83.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 44 481 9157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248880
X-RAY DIFFRACTIONf_angle_d0.500712022
X-RAY DIFFRACTIONf_chiral_restr0.03931269
X-RAY DIFFRACTIONf_plane_restr0.00391565
X-RAY DIFFRACTIONf_dihedral_angle_d11.92333328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.137280.3125105X-RAY DIFFRACTION1.91
2.11-2.160.4022180.2766298X-RAY DIFFRACTION5.38
2.16-2.220.3605160.2778524X-RAY DIFFRACTION9.11
2.22-2.280.3809250.2786522X-RAY DIFFRACTION9.17
2.28-2.360.2755480.261911X-RAY DIFFRACTION16.13
2.36-2.440.2843550.25271252X-RAY DIFFRACTION21.9
2.44-2.540.2963850.26731709X-RAY DIFFRACTION29.96
2.54-2.660.31991200.28162410X-RAY DIFFRACTION42.61
2.66-2.80.28221910.26263459X-RAY DIFFRACTION60.89
2.8-2.970.32792380.24164390X-RAY DIFFRACTION77.52
2.97-3.20.29312450.21095251X-RAY DIFFRACTION91.89
3.2-3.520.25762880.1885696X-RAY DIFFRACTION99.97
3.52-4.030.22942670.15995753X-RAY DIFFRACTION99.85
4.03-5.080.19592520.14865779X-RAY DIFFRACTION99.9
5.08-83.980.19392900.19125850X-RAY DIFFRACTION99.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.641549600276-0.4090266613050.308773949870.478853664503-0.02413087306130.2849712072790.05409390979280.1427166413340.221126688579-0.127227528426-0.0392836571943-0.2302838430290.05947762097380.187499760646-0.006605340411780.141109294310.04896516067170.04276956106110.112092384465-0.01123782081160.40746646479328.1250257914-3.7351155752934.4123310754
23.399659504981.11376243862-2.067611618480.38935252607-0.6325347772951.481710650220.140375316089-0.4311585006050.004048715583710.00323066415795-0.1354368505410.02354377241930.07225225410450.268074137789-0.02471839251980.1697482937070.01288354140770.03488213893090.1182295245980.03012875425940.2414057037318.91412604519.1534533068534.6006385387
30.878477414785-0.6542377497370.3204511282420.944026058693-0.2405814186660.528166969640.04512724391780.0690281161796-0.260131073977-0.0740564708107-0.00768083461183-0.0481821214197-0.0285131807676-0.0126680943695-0.008501164516010.09027145130390.01561244286950.04330493090870.0332389418569-0.02719446498240.2072223252739.24276567829-1.4649333599337.9301319915
40.878755129-0.04278874104930.1780985639780.9693085159110.0653876785310.1644448050990.04155872649390.193964576865-0.0138837456245-0.19813293166-0.0441622893114-0.207588364174-0.05912299987980.05080322372440.007122576402860.1037217505250.05917784949370.05493217074830.0205492917620.01077795198980.31399795482924.92827202740.45608539573438.1898967706
51.353877820960.505064855095-0.8814857848230.8299384871150.179958098721.14001872830.05453930734510.2706266331180.155385529822-0.170972349633-0.05761281251810.370696600321-0.177649258395-0.245958227657-0.02447643365860.1549479180160.0645500779202-0.01614166590660.129393442650.0547997855320.321970727208-19.90846692744.737638472540.4149491864
60.920407036729-0.0682181301862-0.2536013456140.123270597303-0.04903273653450.7995423657350.1214365486820.221920193897-0.212792397179-0.166088213010.006155833186050.296693144760.0227020511046-0.198186805729-0.01100773208180.1467729232160.0302242432797-0.1006315677270.121705669086-0.03393236122020.406092815487-20.525721553928.20210853830.85687747
77.03285660805-0.3264351516240.4174141310191.56590948482-0.3943129758840.1493618440320.0953080174031-0.279255526196-0.0664863179502-0.0491105685668-0.1814864279850.054110385452-0.0929249160884-0.192055584818-0.03888505796980.1297673836570.03210267469970.03914907820970.0951105260753-0.04452339402010.235019230367-11.154877950621.612080482934.6195179711
80.652795251851-0.2676252224210.4902381160310.118758687407-0.2607624792620.7546818881280.04181202905130.04957001869810.0509499499423-0.177852337132-0.08776631049520.02051452922260.2013533042920.0487636717546-0.01485323951930.1321803573960.01434465228930.02341379322690.0327452260529-0.02746102971310.157785263523-0.044777462995924.620549088334.1223065047
90.941796301313-0.624777496714-0.06207172345320.684528510912-0.06917938926822.701774605380.0464550746942-0.02418734384090.150783041133-0.005039729652490.0717538646105-0.07396430913580.1480885226570.211946010467-0.01512296919740.06633332406650.05157475354290.01597706790050.05604395080270.03249430547890.2428377665971.2074293038636.002240807440.7299450185
100.5849233739630.102362397507-0.006927954623780.431248144981-0.1198684008610.25291752741-0.0745113259480.03576080504520.09409290984220.0635149152943-0.01968390325720.188801119953-0.0545261647983-0.0555068634816-0.05524807323660.099016685405-0.0223196000860.01940494774740.0263023419529-0.02267294952430.194274542062-18.431194192731.347312836147.5902766277
112.026074268270.0489512460756-0.8055076872594.846900618882.759948215615.02758439139-0.0425244198498-0.10908311020.183788652995-0.09394798273080.1943591683540.146494073561-0.2192305065680.657014755078-0.1610363706570.1951527267920.0301953954736-0.003621094371220.192812066274-0.0296091277640.189299193728-18.452497799518.180660728755.3541847812
120.261917967508-0.205815025148-0.07670606152660.6657327360740.12278991630.1933662136540.0457865439640.0703573321760.0460888282769-0.110388270459-0.02082249348980.1156420975260.0330623851149-0.02505219035930.008563887894650.07147463556220.0315053493016-0.02864505875010.005686722687030.0314953172310.221918413429-15.297227785836.790232712140.9477371546
132.10345834664.127661932784.322504261258.099036836468.481908237788.88334765764-0.5183424862830.450483320233-0.367395039267-1.208315960871.18566834572-0.276333585885-0.6192714515561.25973962066-0.6000932721190.6942525844050.0640295477602-0.05129399871760.682519603338-0.03878412060310.44965928428-17.412680987320.11106081852.29745624899
140.5811230106620.3542909711890.245158219170.9592589658840.239546720560.905853827575-0.06883352557820.204214718256-0.0413468853326-0.336313297482-0.03279924991660.3212930974170.0183006814965-0.1511720922940.1813690987710.180728041424-0.0189485407077-0.03625301075620.152835988513-0.1277305414320.340880194879-23.82045312431.3802924639926.9394126316
151.9932881588-0.254234611859-0.5708262612560.612092307564-0.1207876506080.229148188029-0.01233922823650.2535607765840.0790162549895-0.305555258006-0.04988249453280.1055946656630.000477865310591-0.08730887132910.08493069421680.171856962894-0.00731628221527-0.0243592412660.0949949722451-0.02527980702750.174511697749-5.888559396529.0792871464127.023430947
161.26336555892-0.4735260500670.3989503728910.946223764499-0.141221543451.85492622245-0.02299141751540.39942337928-0.396574593134-0.373889234992-0.02264275056740.0405614448780.06736574898620.139771840210.03875174563310.219126273377-0.01719225280580.04992493448290.167780969267-0.09679438763250.211272877493-6.15572807116-3.5783091101421.2550622209
174.03710511855-3.49040055422-3.318636413733.24517962373.997250643418.326561287990.427135060349-0.01017274716550.773097640581-0.9197401446730.212474398977-0.55804325514-2.068428227450.0652208799987-0.2682645296341.07594668573-0.0729282878855-0.04183649334660.589969157169-0.09265092551960.362931599896-22.152037803812.71292793056.22200910742
181.058462609920.07232133133270.2091064656431.385500103390.5849953015641.146857214680.01516829201980.320231273205-0.126642462571-0.297677698027-0.04737495774520.132680723238-0.074487729904-0.00797958786664-0.01439321982230.128616905538-0.0362025344134-0.05762628125440.100024190015-0.02513484986990.210321625401-18.60387233952.4660840233728.7423239826
191.87513237444-0.147825670821-0.9457039011220.07563130888160.2465968471110.941827925410.07548757941780.2304757175460.222343165097-0.0825446780817-0.044370338367-0.185232818632-0.17632255470.0384017486888-0.1103945483250.296526098342-0.06698273912790.1411021550150.2469203521260.1177389157160.46682649724633.186548945439.284789923521.0809165937
200.845371689349-0.466745109955-0.011501504690.5602224971080.1627118352010.3933515959970.1122953167450.1269102751250.0516624393056-0.22577591595-0.0905130750987-0.3965928520490.03072421583410.140458151810.2167767335050.1700444056310.04605522049240.05977300703080.1194685511930.05246913707890.49671074651935.436140282222.065469930135.3843810839
212.27051469317-0.391315376032-0.1164086813151.8188618649-0.5747959959670.2081283109780.06519910879880.423680437370.0550211400263-0.4380972559-0.0990611639285-0.4928033932450.161323395471-0.05565158688260.03974863033440.163507001965-0.02749201925980.1142888537250.185842111748-0.0120046213620.38055845047424.552604010624.396379195924.6798823508
223.49374098564-0.8485771271060.6669964442170.723081599434-0.5736813516580.4536065115680.1964495889630.421086915775-0.0107662901152-0.274337812965-0.105339479814-0.1643540075540.1392572166910.126748747354-0.0856969434270.1177500043010.01397834299660.04815499173940.0656963246236-0.02160367956460.17407498400413.734824797721.642138808826.9986954832
232.323747922960.0972930180191-0.6034018288491.225792463520.1764884983631.263000309520.09910480833190.4547866803810.361426959173-0.402023391431-0.117949463844-0.286904606024-0.170728675294-0.09394161917030.06340693577530.2298080845590.06258802816470.04008376793440.1423575791040.06545270127620.24798459636413.959850897934.327408962921.3269834825
246.744423784350.7182366776751.960538895115.21888860103-0.8446706489371.922692098660.3570210155180.877898620342-1.52226418311-1.260700213460.329643689315-0.3733638229311.43518793172-0.195173536273-0.5476021233671.22966626686-0.07377750863420.06411026138630.550716021768-0.05619080894850.69136425830629.658748035418.19118755125.92931420153
253.622961871540.2028216471290.02645888784060.1203261477720.8210925543336.15682785517-0.08444719929990.976153064488-0.328821880001-0.635165633282-0.0650757076172-0.3369058919930.2975382657430.06305110884690.08514033071160.5765692255950.06559194317930.1891090502850.4692216570890.04207069071080.30662148445220.608531785434.2499422859.68060566624
260.646914931452-0.0433147788675-0.1486881976920.401837417954-0.2396874146910.190059918092-0.03032067119670.135918298636-0.0683390660165-0.159617604716-0.0676067458537-0.3736129423960.08811752968280.0665084282087-0.04619627679050.131528036472-0.03025698043520.09849721153950.1358880984770.04473376274190.34062979878331.250849069231.090566112827.0799592508
271.484012475640.789311587756-0.5005788133993.74696628823-1.534495069173.431999718160.252461135196-0.315509983995-0.06386886022670.473249708641-0.2142815176420.1497373552920.2237130687910.03138094364-0.01567281017950.138682748788-0.0816161777662-0.0197417360990.100805743104-0.03188856186840.14251727459425.153483746915.642949653759.1649548657
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 76 )AA1 - 761 - 76
22chain 'A' and (resid 77 through 95 )AA77 - 9577 - 95
33chain 'A' and (resid 96 through 171 )AA96 - 17196 - 171
44chain 'A' and (resid 172 through 266 )AA172 - 266172 - 266
55chain 'B' and (resid 1 through 28 )BB1 - 281 - 28
66chain 'B' and (resid 29 through 76 )BB29 - 7629 - 76
77chain 'B' and (resid 77 through 95 )BB77 - 9577 - 95
88chain 'B' and (resid 96 through 121 )BB96 - 12196 - 121
99chain 'B' and (resid 122 through 159 )BB122 - 159122 - 159
1010chain 'B' and (resid 160 through 184 )BB160 - 184160 - 184
1111chain 'B' and (resid 185 through 196 )BB185 - 196185 - 196
1212chain 'B' and (resid 197 through 249 )BB197 - 249197 - 249
1313chain 'B' and (resid 250 through 266 )BB250 - 266250 - 266
1414chain 'C' and (resid 1 through 76 )CD1 - 761 - 76
1515chain 'C' and (resid 77 through 121 )CD77 - 12177 - 121
1616chain 'C' and (resid 122 through 171 )CD122 - 171122 - 171
1717chain 'C' and (resid 172 through 193 )CD172 - 193172 - 193
1818chain 'C' and (resid 194 through 266 )CD194 - 266194 - 266
1919chain 'D' and (resid 1 through 28 )DH1 - 281 - 28
2020chain 'D' and (resid 29 through 53 )DH29 - 5329 - 53
2121chain 'D' and (resid 54 through 76 )DH54 - 7654 - 76
2222chain 'D' and (resid 77 through 121 )DH77 - 12177 - 121
2323chain 'D' and (resid 122 through 171 )DH122 - 171122 - 171
2424chain 'D' and (resid 172 through 195 )DH172 - 195172 - 195
2525chain 'D' and (resid 196 through 216 )DH196 - 216196 - 216
2626chain 'D' and (resid 217 through 249 )DH217 - 249217 - 249
2727chain 'D' and (resid 250 through 266 )DH250 - 266250 - 266

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