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- PDB-7luy: Crystal Structure of guanylate kinase from Bartonella henselae st... -

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Basic information

Entry
Database: PDB / ID: 7luy
TitleCrystal Structure of guanylate kinase from Bartonella henselae str. Houston-1
ComponentsGuanylate kinase
KeywordsTRANSFERASE / SSGCID / Guanylate kinasem / gmk / Bartonella henselae / Rochalimaea henselae / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / ATP binding / cytoplasm
Similarity search - Function
Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of guanylate kinase from Bartonella henselae str. Houston-1
Authors: Abendroth, J. / Dranow, D.M. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 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
A: Guanylate kinase
B: Guanylate kinase
C: Guanylate kinase
D: Guanylate kinase
E: Guanylate kinase
F: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,04525
Polymers169,5266
Non-polymers1,51919
Water5,603311
1
A: Guanylate kinase
F: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9557
Polymers56,5092
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-78 kcal/mol
Surface area19240 Å2
MethodPISA
2
B: Guanylate kinase
E: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,16911
Polymers56,5092
Non-polymers6619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-63 kcal/mol
Surface area19340 Å2
MethodPISA
3
C: Guanylate kinase
D: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9217
Polymers56,5092
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-64 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.820, 101.910, 86.660
Angle α, β, γ (deg.)90.000, 115.982, 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
Guanylate kinase / / GMP kinase


Mass: 28254.342 Da / Num. of mol.: 6 / Fragment: BaheA.00713.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: ATCC 49882 / DSM 28221 / Houston 1 / Gene: gmk, BH05390 / Plasmid: BaheA.00713.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6G439, guanylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents JCSG+ screen, condition H9: 200mM lithium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BaheA.00713.a.A1.PS00367 at 20mg/ml: tray 205529 H9: cryoprotectant: 25% ethylene glycol: puck: ekw2-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 59593 / % possible obs: 99.7 % / Redundancy: 4.574 % / Biso Wilson estimate: 46.792 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Χ2: 0.902 / Net I/σ(I): 19.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.364.6160.6222.5943890.7860.70199.8
2.36-2.424.620.5323.0442700.8320.699.8
2.42-2.494.620.4633.541620.880.52299.9
2.49-2.574.620.3724.2740620.9130.41999.8
2.57-2.664.6280.2935.4638890.9440.33199.7
2.66-2.754.5980.2396.8637910.9610.26999.8
2.75-2.854.6150.1978.2437050.9730.22299.8
2.85-2.974.6220.14410.8635120.9850.16399.7
2.97-3.14.6160.10914.0833850.9910.12399.9
3.1-3.254.6040.08418.0632490.9950.09599.8
3.25-3.434.5990.06323.2530650.9970.07199.6
3.43-3.644.5530.0492929110.9980.05599.7
3.64-3.894.4730.03735.2527340.9990.04299.8
3.89-4.24.4860.02943.1925470.9990.03399.3
4.2-4.64.5060.02549.2123610.9990.02999.7
4.6-5.144.4720.02550.3821370.9990.02899.5
5.14-5.944.3850.02844.818750.9990.03199.8
5.94-7.274.5290.02744.9916060.9990.03199.4
7.27-10.294.5110.01662.35125110.01999.2
10.29-504.2230.01567.6669210.01797.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2f3t in two domains as per Morda
Resolution: 2.3→45.71 Å / SU ML: 0.3185 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 2017 3.39 %0
Rwork0.1984 57564 --
obs0.2002 59581 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9236 0 86 311 9633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00579511
X-RAY DIFFRACTIONf_angle_d0.73912854
X-RAY DIFFRACTIONf_chiral_restr0.04561449
X-RAY DIFFRACTIONf_plane_restr0.00651644
X-RAY DIFFRACTIONf_dihedral_angle_d13.67713428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.29571560.25534082X-RAY DIFFRACTION99.93
2.36-2.420.26111520.24144091X-RAY DIFFRACTION100
2.42-2.490.31831310.23914106X-RAY DIFFRACTION99.98
2.49-2.570.30851320.2364092X-RAY DIFFRACTION99.95
2.57-2.660.31931520.24724094X-RAY DIFFRACTION99.93
2.66-2.770.3011780.22994065X-RAY DIFFRACTION99.93
2.77-2.90.28041960.21714038X-RAY DIFFRACTION99.95
2.9-3.050.24291780.20344076X-RAY DIFFRACTION99.95
3.05-3.240.2931230.214127X-RAY DIFFRACTION100
3.24-3.490.2243850.19534172X-RAY DIFFRACTION99.88
3.49-3.840.25361070.18484141X-RAY DIFFRACTION99.91
3.84-4.40.21911570.16644110X-RAY DIFFRACTION99.86
4.4-5.540.21571470.17664138X-RAY DIFFRACTION99.88
5.54-45.710.24211230.19184232X-RAY DIFFRACTION99.7
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)
11.49059858016-1.336019086422.423190806384.054023198660.7455879569776.69245831881-0.0798965124816-0.2268943902740.406371444458-0.0822522683893-0.1855385746670.347306515555-0.812698379925-0.3222797522170.2064628460510.2840107623140.01434698003260.06978598352160.3240605222310.000498517219390.420981340285-1.235756615263.959301683753.7586969007
22.476184837270.0821004346440.5457643131272.329231234420.5567473481263.594879275790.0259888474067-0.1812480501690.006040805822540.1619169726130.174222578190.016830577705-0.1274942848740.230770862363-0.2019762255370.196051906099-0.01183044693570.07964164255030.302868366502-0.0009589049523640.3155741403397.8958534316957.945744308357.7884315098
33.31753455154-2.41714274914.638259026618.69359401573-1.704355645416.89285868942-0.307987538675-0.890369125730.3365375865290.7822765492910.8073979973290.134420787229-1.919826806070.322753003198-0.3886839556260.645865743043-0.01636718969420.1841764614460.801039793734-0.1019875428610.58953071534412.805163010281.85770271251.2277987577
48.010530876282.323182181771.238063244272.56425358002-0.04578353205013.12287289940.03239262755730.1194633475460.1078782091190.1177423597950.1004669322220.281313292114-0.33156467302-0.0307284777807-0.05915009616440.301354930070.04126401432240.03386603830890.2828404426110.07980092385260.226699249549-1.7975243587162.522230361743.7312157995
54.19616807911-1.359724716982.267311854562.84085802639-0.9239042607746.795767290150.2132147527270.8404526644320.268889776174-0.672024318566-0.24994149988-0.139997291928-0.1604284598360.4705083420760.009130580179730.4397236346870.03514563735240.06420425013620.3453788500140.005254633684460.345200167497-44.17435247743.667664519553.2901725627
61.58089381335-0.7657516581611.307155359621.99063334708-0.6283557343352.01476956731-0.03091333076550.1468480540060.0946953563048-0.179982087627-0.0572348056612-0.116258919995-0.1945603754750.05087638662560.08383703188370.279559805344-0.006275285519760.01478556567280.246253487105-0.002854739355440.303710139884-40.731503038846.090975583564.993782388
73.830541290960.840528633441.319244516282.586301409180.3059589967790.9117917474110.548578872313-1.14186549748-0.4003775058481.00148002309-0.411578504878-0.1684723405880.0374930664086-0.23207424335-0.1382148489580.647855262164-0.208586800536-0.02736418118920.6243408731960.09929112854090.34079253841125.333432813428.348813329784.6315028804
86.575191795931.539359470322.325374734024.17249362795-0.9144680145341.842427755530.0631393118032-0.9391154414050.217037629350.675913030369-0.0286200206858-0.0715378375946-0.274881879047-0.1833597577040.000188772407540.429268686741-0.0329587087174-0.003396542970650.409287461097-0.03305315150510.33007131952128.48346634833.966185135479.4326741104
92.39421790135-0.149062020648-1.218954376631.959876491041.173717109654.404147666950.295164583032-0.2969350607970.1123111766930.324271847053-0.1720958450060.116569699446-0.46497591127-0.02727440336-0.1139655566330.333878506367-0.02547682602660.01936497840620.2959098604130.029715538640.27630854164413.476169494331.210360524274.3268595219
102.417706767930.2603018931852.93692243785.848084389541.616076736645.401033629910.06318712096930.135693752809-0.2514653062280.184573725876-0.01559526743740.0885859571480.43304334937-0.5460875344570.09559334931180.197916367746-0.09020870739870.009686304503010.2982562965970.04533543722880.3336827007244.8728165903729.15657469655.130321572
113.490144282171.265237284092.851448977643.132333360230.04669706561234.21257905323-0.3074935041680.3611089213-0.34264363303-0.3401371406770.219015158106-0.0213656779606-0.09193542980280.02619310459990.1217637989050.27348808314-0.04318287086480.08205725078440.372287440343-0.00655386342760.395568308762-1.0441482615931.190339292543.8985797999
122.95955150648-1.53492648321-0.3099000214213.895120902270.899213891663.000053522540.0235856429510.508171509628-0.617557844402-0.06698753381940.04458025569650.4506453719220.6444075910990.142186177345-0.1080395685240.280989311357-0.006926621807-0.03567310752150.379415101946-0.06620202945720.31732621244712.38302001417.784364189946.6248743243
132.87800322621-2.00130749848-0.879324044114.33121437672.898058589058.330009800270.1585772730420.2287448914250.06755178632870.0573722096119-0.08874765243880.128874798305-0.00592715587738-0.08961219515960.02085836580660.145798808608-0.01808773876890.0106335560120.3020691276250.05249903565290.26486074070510.47392707727.512584231658.0615158515
142.710226688170.88278270821-1.247862117116.90035095733-4.374802747164.444492336430.2444248899360.08154214573240.5357538699250.3188718332-0.3546491660670.435025458179-0.5539258579480.5075726510760.04382645044190.487258262563-0.0436899877227-0.2349000857340.298424289438-0.01662988107450.637268369817-26.845709834849.162978372983.6401837535
152.16633688712-2.333598720731.904783471553.61298359644-3.344781169323.186487643990.4685238266550.901741009025-0.552802000132-0.485648830987-0.707453350083-0.3934483176810.8177482425780.9908529141770.09398058197140.6923756901380.0114708254458-0.1128580055850.5645636403280.06797038437060.641152831955-16.524756802236.450529365783.2828924709
165.48742593384-1.4722803429-4.333141062345.239535374785.41338608018.96774788366-0.000147697927683-0.8761394874340.5936908714190.6800155964490.134280413855-0.402388777152-0.1397729369912.48473988272-0.1120399230480.66628066502-0.0673041142384-0.3508764426520.8961080383470.09459567572630.803443188231-17.101089764550.208981850287.7332614
176.713009138213.08998661371.809808542656.834933024053.398957088196.104468603210.502986594204-1.33669521798-0.07585107434510.460417291859-0.705923787031-0.0621126050519-1.316008559271.034402632020.1340894754711.16698162606-0.244206157955-0.2902984945851.0550582673-0.2121568565510.762254137017-13.157314474449.1544462276102.96675844
184.095307991643.555572364920.8697698368117.431527054790.9921338464635.56560435370.0932974045157-0.815831403953-0.07630415297082.023441163290.0654997542174-0.0622181645034-0.236665062131-0.217689607447-0.2025151649651.23135757296-0.140250768611-0.04859126503540.683838461846-0.195574578950.962266311268-25.724486012847.5825493136105.391833374
195.04451511072-0.0721944349317-0.7408255172673.683836557570.9765803573753.22811563384-0.0332094013039-0.742466451851.003740201730.77917198707-0.168963883442-0.963411049697-0.833665066930.7386249001270.02169944467291.00201709275-0.090660013491-0.1299370095620.575396467742-0.2064408833960.831774114931-23.811717498553.273348867595.0919354777
203.91732179769-1.750163865280.6090375417593.676298260351.726784636344.415220617620.169507918122-0.4248449516490.2601807642261.04822100537-0.195260556199-0.345080519062-0.1055593898630.469077778731-0.0008211997296860.607850059802-0.0330859672098-0.206456551620.318120049608-0.05033363770490.473393042049-27.167456254844.078061564191.2704801148
213.60888866028-1.273358207070.6524631599783.17569447392-0.9912556495531.402562887210.122009829158-0.0214109161559-0.446274340021-0.284252241216-0.1517531574680.1383861833780.1085968433580.3041047306030.09568803800530.3622095315690.0130654864847-0.07184414265430.2976854403650.05317107326170.417144077258-19.521562908629.926000202385.8083180587
222.49986040742-2.231482765941.19406274822.85669470738-2.140808438621.900273044630.0439531935647-0.227774570262-0.2207633491490.441100802662-0.0223664071113-0.322386363750.1991114057960.1633994057560.08481282135340.562843123637-0.0561935479395-0.1580723066960.3048726563010.001910094811040.481376072419-25.271011095728.124863398688.3053357159
234.04407230581-5.375816395992.640429542028.99335314283-2.800802757922.27533043011-0.251314496586-0.06559357862260.3351527507890.184746341527-0.0172612113392-0.835107683862-0.2926592124960.1356820295140.3514547641450.280786725059-0.0470114318879-0.06865059130370.2748416151060.03968218618270.420573852425-31.471414718954.253602167672.6918712047
240.9325758344140.2719672571981.289490575076.153806025270.300166197929.43852444101-0.1890365866390.365542136915-0.134375655926-1.50507150859-0.0842737073581-0.109712904467-0.0261185774027-0.3820462849370.2886584382770.641485355943-0.01175357340920.01420352949620.6279857316420.01905468852180.431280089856-14.522516595761.657757846418.9686087638
255.473890129441.922166343431.753005066351.644183826140.9127388423851.6278387226-0.00196182703320.378191671356-0.142554594892-0.1691883825330.03767103233620.277260457106-0.0604939550185-0.0827902697313-0.009352543726360.3158139873160.0519624602352-0.02855610995520.3628225163840.06396026577040.365199590284-14.47256514758.573126642131.9882924181
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 52 )AA15 - 521 - 38
22chain 'A' and (resid 53 through 140 )AA53 - 14039 - 126
33chain 'A' and (resid 141 through 155 )AA141 - 155127 - 141
44chain 'A' and (resid 156 through 221 )AA156 - 221142 - 207
55chain 'B' and (resid 15 through 79 )BF15 - 791 - 65
66chain 'B' and (resid 80 through 221 )BF80 - 22166 - 202
77chain 'C' and (resid 16 through 79 )CJ16 - 791 - 64
88chain 'C' and (resid 80 through 126 )CJ80 - 12665 - 111
99chain 'C' and (resid 127 through 221 )CJ127 - 221112 - 204
1010chain 'D' and (resid 15 through 31 )DL15 - 311 - 17
1111chain 'D' and (resid 32 through 126 )DL32 - 12618 - 112
1212chain 'D' and (resid 127 through 155 )DL127 - 155113 - 141
1313chain 'D' and (resid 156 through 219 )DL156 - 219142 - 205
1414chain 'E' and (resid 16 through 26 )EQ16 - 261 - 11
1515chain 'E' and (resid 27 through 39 )EQ27 - 3912 - 24
1616chain 'E' and (resid 40 through 52 )EQ40 - 5225 - 37
1717chain 'E' and (resid 53 through 70 )EQ53 - 7038 - 49
1818chain 'E' and (resid 71 through 91 )EQ71 - 9150 - 70
1919chain 'E' and (resid 92 through 107 )EQ92 - 10771 - 86
2020chain 'E' and (resid 108 through 126 )EQ108 - 12687 - 105
2121chain 'E' and (resid 127 through 155 )EQ127 - 155106 - 134
2222chain 'E' and (resid 156 through 184 )EQ156 - 184135 - 163
2323chain 'E' and (resid 185 through 221 )EQ185 - 221164 - 200
2424chain 'F' and (resid 16 through 107 )FX16 - 1071 - 76
2525chain 'F' and (resid 108 through 221 )FX108 - 22177 - 190

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