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- PDB-7lwz: Apo Structure of Vibrio cholerae dGTPase protein VC1979 -

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Basic information

Entry
Database: PDB / ID: 7lwz
TitleApo Structure of Vibrio cholerae dGTPase protein VC1979
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase-like protein 1
KeywordsHYDROLASE / METALLOENZYME / METAL BINDING PROTEIN
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process
Similarity search - Function
dNTP triphosphohydrolase, type 2 / Phosphohydrolase-associated domain / Phosphohydrolase-associated domain / dNTP triphosphohydrolase / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
NICKEL (II) ION / Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSikkema, A.P. / Horng, J. / Klemm, B.P. / Schaaper, R.M. / Hall, T.M.T.
CitationJournal: To Be Published
Title: Structure of Vibrio cholerae dGTPase protein VC1979
Authors: Sikkema, A.P. / Horng, J. / Klemm, B.P. / Schaaper, R.M. / Hall, T.M.T.
History
DepositionMar 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
A: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
D: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
C: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
F: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
E: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,31112
Polymers300,9596
Non-polymers3526
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16430 Å2
ΔGint-116 kcal/mol
Surface area95290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.003, 161.869, 184.773
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
Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1


Mass: 50159.805 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1979 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KQL9
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Description: Crystal were approximately 200um with an orthorhombic pyramidal morphology. Grew under precipitate.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein solution (15mg/mL dGTPase, 50mM Tris pH 7.9, 100mM NaCl, 10% glycerol) mixed 1:1 with well solution (0.95M NaCl, 7mM NiCl2, 0.06M Na Acetate). Cryo condition was well solution with ...Details: Protein solution (15mg/mL dGTPase, 50mM Tris pH 7.9, 100mM NaCl, 10% glycerol) mixed 1:1 with well solution (0.95M NaCl, 7mM NiCl2, 0.06M Na Acetate). Cryo condition was well solution with 30% ethylene glycol added.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2019
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→37.86 Å / Num. obs: 270862 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 65.21 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.088 / Net I/σ(I): 11.15
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 42766 / CC1/2: 0.481 / Rrim(I) all: 1.64 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PGS
Resolution: 2.32→37.86 Å / SU ML: 0.4081 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 11887 4.58 %
Rwork0.2184 247401 -
obs0.22 259288 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.38 Å2
Refinement stepCycle: LAST / Resolution: 2.32→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18255 0 6 132 18393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009218654
X-RAY DIFFRACTIONf_angle_d1.14925280
X-RAY DIFFRACTIONf_chiral_restr0.15242784
X-RAY DIFFRACTIONf_plane_restr0.00843303
X-RAY DIFFRACTIONf_dihedral_angle_d25.01876752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.3883620.39927515X-RAY DIFFRACTION89.41
2.35-2.370.37013940.39038212X-RAY DIFFRACTION98.56
2.37-2.40.39353940.37728286X-RAY DIFFRACTION98.83
2.4-2.430.38744000.3678279X-RAY DIFFRACTION99.2
2.43-2.470.3633990.36088314X-RAY DIFFRACTION99.14
2.47-2.50.3773950.34368326X-RAY DIFFRACTION98.53
2.5-2.540.35363910.33528107X-RAY DIFFRACTION98.21
2.54-2.570.32353990.31548215X-RAY DIFFRACTION97.98
2.57-2.610.3333970.31378315X-RAY DIFFRACTION99.65
2.61-2.660.34983980.30878347X-RAY DIFFRACTION99.94
2.66-2.70.33164040.30338395X-RAY DIFFRACTION99.98
2.7-2.750.29433990.29068329X-RAY DIFFRACTION99.93
2.75-2.80.31974090.27518378X-RAY DIFFRACTION99.84
2.8-2.860.32834010.26568311X-RAY DIFFRACTION99.9
2.86-2.920.28574060.25918379X-RAY DIFFRACTION99.8
2.92-2.990.31074050.25528365X-RAY DIFFRACTION99.83
2.99-3.070.31654030.27078337X-RAY DIFFRACTION99.81
3.07-3.150.31763990.27238299X-RAY DIFFRACTION99.44
3.15-3.240.33174000.26048308X-RAY DIFFRACTION99.37
3.24-3.350.26363990.24278282X-RAY DIFFRACTION99.25
3.35-3.470.29473890.23738303X-RAY DIFFRACTION99.03
3.47-3.610.25144020.23028227X-RAY DIFFRACTION98.24
3.61-3.770.24253860.19738041X-RAY DIFFRACTION95.99
3.77-3.970.25083980.20178251X-RAY DIFFRACTION99.11
3.97-4.220.2383950.1818306X-RAY DIFFRACTION99.04
4.22-4.540.19493920.16678263X-RAY DIFFRACTION98.88
4.54-50.19413930.17328296X-RAY DIFFRACTION98.74
5-5.720.26263900.19878223X-RAY DIFFRACTION98.58
5.72-7.190.22243930.20538058X-RAY DIFFRACTION96.38
7.2-37.860.17633950.16658134X-RAY DIFFRACTION97.15
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)
12.395687246470.2459164048190.7907126517232.84252458563-0.1546274069372.62483804433-0.0569641146616-0.1370931244250.2307542175330.4280098527570.0336134149348-0.0772571135253-0.2135450557430.1298324202220.005898591631220.465334768798-0.0146830496809-0.05480732269440.398797725471-0.0191507802880.38660100560183.7417935776112.64886668570.9511794616
24.88033056766-6.10144638279-0.03826666298589.992612626151.123314228356.50070262521-0.009258414236520.119323543994-0.1466774442410.4716524627210.271146258607-2.581596243180.08600124121270.599198491363-0.3490777840390.658480420871-0.0468647441465-0.1350513132820.932560896223-0.03536938664120.97615065260994.8720812182107.41928710657.7590593119
30.618254711602-1.277227260171.454021064492.87373576455-4.406780037568.52430217912-0.05541187907710.2194433371060.307661873976-0.360686401410.0507407846487-0.1173175619750.2415793709660.505894257808-0.0006114056806240.639527825008-0.0728142512831-0.08504104888660.733754270395-0.04533746861040.58454741864693.7611082035112.32731901270.2941597073
41.428212375190.0636568526340.7110219844281.927401846390.4580326165942.614274427650.113623347649-0.122046611871-0.08501723011120.409362290559-0.0645606660942-0.2880539223150.3236774351640.292985556606-0.09185960261730.5122025207120.0083462123505-0.02636822419430.505317145409-0.007795092675950.50387112675890.712226373497.585536437871.8099243959
52.39397548861-0.618830194290.1812685434253.679719948150.1037203376462.05574688848-0.00202248124592-0.209658396973-0.03393291836040.2745529844930.102952242550.113872248662-0.05561088251590.12618728737-0.08142194219710.6675809187850.03781821002080.09607216437740.506742652131-0.04036297840860.46829298667769.0717337569102.58139675491.5468353893
60.7565830803050.1198466814571.109015893431.74853182579-1.937237704944.636709763830.0326038899735-0.2726823004410.1193224372110.6014826905830.1895658726270.515796606021-0.0816199532992-0.0909955554436-0.2783824945370.7244537210170.08324158642110.2276971976670.6230276772950.03205106540620.76193181977759.1835556665105.01337000694.5619152754
72.59629639027-0.759784649170.3159316327173.35149243191-0.01263814792391.855779260620.1915315965330.1798304031710.0355502087429-0.370221764629-0.1458564675910.2126964026120.0946812051774-0.0553254256444-0.04588782902590.514574130515-0.007433680279390.02354525272780.469051436158-0.02536235427610.44739749930251.934067553977.623595507527.0321243607
89.760942362912.106926076468.982131046196.393901134781.032311731238.84413960085-0.6533707430541.322175312432.05684939969-1.092939622-0.0977198544810.544858198395-0.7357966352581.299157240480.6558490843040.7240639691880.04365527078850.1739016642810.8896514292030.1637345821320.95957053811370.5994897887.687571400226.6160173494
93.02772046123-1.67436921628-1.229840909024.416245928033.188857755314.40156124316-0.009848435586960.5084389705230.10906802725-0.7926640985540.0106258036323-0.2661094473430.1726119645440.515900077829-0.04777705147850.6821525311670.04107540352210.02699809378030.565239453680.0743179991670.57613090575654.092720734586.297436182522.3206852346
102.44758158855-1.252038781830.3471231323513.24938937106-0.1863854318390.616031999713-0.09063861127110.01125609809280.270194468868-0.02971703721390.113050358875-0.155529185983-0.0539824052109-0.00802961713608-0.01345807168840.475844453806-0.0488662816923-0.0003292182639470.490233399980.0161146111990.47580063027257.161192364489.105684726236.5275675382
111.267996919480.182896299910.8048041077772.848483516270.5497054867362.78633892995-0.0423991483982-0.04884000593540.0720396987088-0.0603437731462-0.006479023133530.5297810103690.148810741418-0.2239374382880.04551583436040.477955865691-0.02868760140690.08456964191560.5265711511750.02672711051460.67935571753633.071016872774.605945986446.7175563425
129.18982188271.471539353135.366756820957.0963661647-0.3417206698153.39936111270.703846432734-1.74350535968-0.288238743460.33686564586-0.1873333290390.7718578849761.524215604450.150068750871-0.5783971560530.909445757851-0.01746238276840.1582481352340.9297285134390.1189147523060.85298255946632.08559529864.541724010864.5999811504
131.84284079621-0.4382457023350.03372047527084.82553779896-0.6020022124171.76463084668-0.184773946483-0.0490094523737-0.0366780658939-0.3517218351920.0428021113441-0.8386268381670.2019954641130.3077098044750.1628193594430.446562443973-0.01809376454870.1230481689460.55958509708-0.003877469910360.83748832169899.726496675549.251224608661.8962161924
141.56555604708-1.49190283803-1.170072027045.96584071826-2.872674321364.38574001187-0.0789724531264-0.660782003618-0.328962582988-0.895542189891-0.793346063887-1.107970165870.8554109620490.5330376096780.7700031507810.562156034666-0.1380070158840.3255092987410.661694560597-0.05533717184081.21808556872102.62503849158.246843409149.1591915589
154.756283660593.834889754271.754140789334.356902427220.03943622553421.88874124785-0.1816769323020.08029141560720.295559299079-0.7687813971550.0204189011302-0.8710360110330.1728376244640.403086244050.1388983407940.820386636747-0.05589935862390.3006687419680.6505422854130.001179192935710.882710141978100.91174288446.49116440153.2060178691
162.51930578408-0.4927688180420.2201217805393.85977643808-0.3667710211432.41644357054-0.0237549430501-0.05754569722-0.2275374126050.16513857880.0791137642186-0.08988006730060.1626028476740.140996334663-0.03320095622110.424181769041-0.0178421607815-0.01322290142990.4859026250820.002253726661160.54645435145779.181455199339.41183176776.8949102672
179.37132451637-7.38366661531-2.614263785245.878148301071.658786665896.16216876976-0.834716934786-0.824539561508-0.5471936052450.9472513730880.4796644222260.983133428320.368477595489-0.2522076161230.3708018696770.6900946577830.01516861050420.07767402677990.7510666833910.05138871388440.86882169002563.895674889449.42051372491.5181595738
184.760460156461.075833084430.5968208193162.614381284991.483182684190.605362694689-0.311884143813-0.2984395976390.1175917081460.5390217791650.3509593085040.4131359211770.264486859506-0.0209515297954-0.05304215868310.7971752537250.044690486896-0.0567609511480.8098123116680.06165301768320.69611222154878.984409353239.380583547787.5175276065
199.414589043916.109392039653.960994162495.136580445264.852050838776.028179249520.5086760949180.1249403924241.149413562230.953004205773-0.535650610971.976432494940.350052064816-0.4308388565420.2638345822630.910286878160.03385878560350.214379046190.7090807266160.1532873509741.1967289854851.104589090588.480075898992.8696750005
200.95873956964-0.231800253680.5446455829391.89923236745-0.7390477049181.406906362730.0381783311744-0.179576394364-0.05246966862120.1333465695480.174312421450.57839277887-0.00143477119818-0.207152526873-0.222853202690.4756431232570.007526655422220.1002031247870.4250542198880.01710419129940.58159669508358.609172718999.574522230780.9405592528
212.58143374994-4.41847772816-2.28816345087.957816414643.680380775833.463478055510.117228763725-0.6307931231580.402402352520.379658500710.203067929291-0.08228234997740.2824572766150.104816063558-0.3220298497790.655154131545-0.103152251830.07123190758590.575428317799-0.03413124014170.83613897207129.044895572365.229929380949.8625851091
221.263505243960.8468265581170.8941187816214.47233142281.575084793592.140337527510.02043703462130.135599567248-0.1999700502860.2151666631080.227151109667-0.1105401327660.1875191224540.117089077603-0.2785743629160.374386435823-0.0612442201050.07084686269480.4130741963650.03398444909590.48494177376343.370285984362.688580646251.9736584787
231.166659201720.4645165570310.05266342187723.54164344858-0.1167974112511.24028679876-0.2617510063590.230624200964-0.100821814666-0.7021670175360.169563922507-0.2529603793530.2213634104240.1341815543310.07510015139490.662268350236-0.0396970006080.0753026710030.491519355123-0.01017571864890.50959149549587.839451546852.305016272451.3225179412
242.56079306291-0.814576914280.9691807336322.51982338512-0.1247607902381.66233907707-0.215418303336-0.3856006992880.3100564069170.4880888974920.0840085427793-0.218652365281-0.06115123938150.07603833345090.1538634165550.5483842310450.02999959182240.01528037287960.539688479607-0.04865757858940.54466213354780.200195354154.042083199484.0629298165
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 5 through 167)BA5 - 1671 - 151
22chain 'B' and (resid 168 through 198)BA168 - 198152 - 161
33chain 'B' and (resid 199 through 264)BA199 - 264162 - 213
44chain 'B' and (resid 265 through 436)BA265 - 436214 - 385
55chain 'A' and (resid 6 through 167)AB6 - 1671 - 150
66chain 'A' and (resid 199 through 264)AB199 - 264173 - 229
77chain 'D' and (resid 5 through 167)DC5 - 1671 - 150
88chain 'D' and (resid 168 through 198)DC168 - 198151 - 167
99chain 'D' and (resid 199 through 264)DC199 - 264168 - 221
1010chain 'D' and (resid 265 through 435)DC265 - 435222 - 392
1111chain 'C' and (resid 6 through 167)CD6 - 1671 - 147
1212chain 'C' and (resid 168 through 198)CD168 - 198148 - 162
1313chain 'F' and (resid 6 through 167)FE6 - 1671 - 146
1414chain 'F' and (resid 193 through 198)FE193 - 198147 - 152
1515chain 'F' and (resid 199 through 264)FE199 - 264153 - 201
1616chain 'E' and (resid 8 through 167)EF8 - 1671 - 149
1717chain 'E' and (resid 168 through 198)EF168 - 198150 - 174
1818chain 'E' and (resid 199 through 264)EF199 - 264175 - 229
1919chain 'A' and (resid 168 through 198)AB168 - 198151 - 172
2020chain 'A' and (resid 265 through 435)AB265 - 435230 - 400
2121chain 'C' and (resid 199 through 264)CD199 - 264163 - 218
2222chain 'C' and (resid 265 through 436)CD265 - 436219 - 390
2323chain 'F' and (resid 265 through 436)FE265 - 436202 - 373
2424chain 'E' and (resid 265 through 435)EF265 - 435230 - 400

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