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- PDB-10sw: Crystal structure of Guanylate Kinase from Burkholderia thailande... -

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Basic information

Entry
Database: PDB / ID: 10sw
TitleCrystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP
ComponentsGuanylate kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Guanylate Kinase
Function / homology
Function and homology information


guanylate kinase / GMP kinase activity / ATP binding / cytosol
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
GUANOSINE-5'-DIPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionFeb 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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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
G: Guanylate kinase
H: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,06718
Polymers193,6358
Non-polymers4,43210
Water1629
1
A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers48,4092
Non-polymers1,3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-36 kcal/mol
Surface area20320 Å2
MethodPISA
2
C: Guanylate kinase
D: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2954
Polymers48,4092
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-30 kcal/mol
Surface area20080 Å2
MethodPISA
3
E: Guanylate kinase
F: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers48,4092
Non-polymers1,3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area20100 Å2
MethodPISA
4
G: Guanylate kinase
H: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2954
Polymers48,4092
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-38 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.155, 63.261, 191.804
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Guanylate kinase / GMP kinase


Mass: 24204.328 Da / Num. of mol.: 8 / Fragment: v18-224P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Gene: gmk, BTH_I1586 / Plasmid: ButhA.01463.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2SY72, guanylate kinase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, ...Details: 1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 15, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.96→47.77 Å / Num. obs: 47978 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.11 / Net I/σ(I): 16 / Num. measured all: 325948
Reflection shellResolution: 2.96→3.04 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.342 / Num. measured all: 24084 / Num. unique obs: 3547 / CC1/2: 0.574 / Rpim(I) all: 0.555 / Rrim(I) all: 1.454 / Χ2: 0.96 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→47.05 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 2378 4.96 %
Rwork0.2023 --
obs0.2051 47955 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12788 0 280 9 13077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313379
X-RAY DIFFRACTIONf_angle_d0.60818228
X-RAY DIFFRACTIONf_dihedral_angle_d20.8634763
X-RAY DIFFRACTIONf_chiral_restr0.0412028
X-RAY DIFFRACTIONf_plane_restr0.0052326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.020.43471250.33842690X-RAY DIFFRACTION100
3.02-3.090.40021200.32562675X-RAY DIFFRACTION100
3.09-3.160.35581380.31412666X-RAY DIFFRACTION100
3.16-3.240.36771290.30152653X-RAY DIFFRACTION100
3.24-3.320.33591540.25982659X-RAY DIFFRACTION100
3.32-3.420.29841460.23812626X-RAY DIFFRACTION100
3.42-3.530.26921280.24032700X-RAY DIFFRACTION100
3.53-3.660.3011370.23282647X-RAY DIFFRACTION100
3.66-3.80.28561510.22462667X-RAY DIFFRACTION100
3.81-3.980.25971370.20922670X-RAY DIFFRACTION100
3.98-4.190.23481250.18052686X-RAY DIFFRACTION100
4.19-4.450.24251390.1672664X-RAY DIFFRACTION100
4.45-4.790.20511670.15892696X-RAY DIFFRACTION100
4.79-5.280.2231590.16222668X-RAY DIFFRACTION100
5.28-6.040.25051400.19092681X-RAY DIFFRACTION100
6.04-7.60.25681560.21052705X-RAY DIFFRACTION100
7.6-47.050.23081270.17192824X-RAY DIFFRACTION99
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)
12.59110.014-0.75876.77530.55028.7456-0.27620.3818-0.2528-0.611-0.1310.25720.20160.81470.3940.7928-0.0828-0.02590.48240.07530.445940.7654-43.286877.0905
24.89630.27270.52467.11582.69458.22160.2248-0.8662-0.60480.2028-0.2484-0.16330.933-0.3893-0.05720.7619-0.0323-0.06270.78570.21730.622340.8269-49.74185.5686
35.7486-4.1123-1.11167.26681.6140.4140.3303-2.57330.41711.88320.63870.47720.58710.0836-0.67010.98520.1619-0.23851.03930.03021.105250.4187-60.973784.6491
41.5650.3673-1.06895.02251.54332.8357-0.09610.3043-0.3068-0.52770.2694-0.4160.33680.3373-0.18950.9173-0.04910.02850.7274-0.09330.794545.7398-50.766672.7649
57.3693-3.81460.77838.28260.72866.559-0.9616-2.7198-0.2654-0.12431.31.7073-0.48650.045-0.38760.5923-0.09330.02511.25150.23360.749163.5779-42.574291.1981
69.4723-2.59380.59193.7453-1.51244.10810.39-0.1071-0.1093-0.0922-0.2043-0.1866-0.15440.0882-0.14490.819-0.1191-0.15180.4945-0.05470.428550.5096-38.960784.4264
72.1259-0.48370.40034.99091.06745.1925-0.25910.4873-1.67630.55430.09670.17840.87850.10040.040.7551-0.0732-0.20340.84980.03130.746521.168-34.877473.1582
85.3106-0.14784.76373.0165-0.6645.8379-1.0094-0.878-0.4904-0.6266-0.6589-2.0609-2.4984-0.14141.60971.3129-0.1584-0.17680.62350.17061.118948.0072-19.21275.6358
92.56610.6594-1.4197.8155-2.28344.6770.2363-0.88330.38260.43820.1248-0.1343-0.54720.1386-0.37250.6965-0.04180.02840.6795-0.02860.495729.3995-16.92686.6933
105.9405-0.9617-1.6634.76940.4936.61850.01950.1056-0.0055-0.2845-0.0517-0.0224-0.54710.0184-0.02080.9452-0.0612-0.18540.61420.14830.733224.3339-2.726479.43
113.9939-1.6484-0.25054.4785-0.33935.57310.7321.26550.8155-0.6874-0.6827-0.6851-0.26790.9974-0.19450.8847-0.1918-0.08430.75640.07280.723834.8911-7.98178.7787
120.773-0.12440.78465.34350.41414.0355-0.02970.41840.5542-0.34430.5068-0.1838-0.44190.334-0.19750.7563-0.0728-0.09160.61090.03050.51230.5912-19.067276.4566
139.7907-1.56580.35696.10222.91135.11060.2645-2.1380.67870.2475-0.09291.2925-1.05680.5780.27881.0979-0.3849-0.09361.10650.08750.77656.4956-21.854782.3141
142.7616-4.42440.33466.8285-0.53134.5069-0.25170.29281.8011-0.01950.3355-0.4574-0.0104-0.3136-0.07660.8449-0.1097-0.05760.7663-0.04020.718811.8984-19.858273.296
156.7227-1.51162.34342.34470.95862.69390.5705-0.5795-0.24450.2855-0.2880.41020.3701-0.6952-0.16640.7603-0.0713-0.0630.65730.11860.559329.2355-29.204785.8146
168.6849-1.35840.4892.9410.84922.49310.3205-0.10390.4177-0.23440.3117-0.0622-0.50660.5559-0.59420.8391-0.09980.04330.8378-00.772553.9337-27.364281.1745
179.8987-0.0251-0.02095.5712-0.57964.7786-0.0075-0.4588-0.7771-0.01230.01590.06920.4293-0.214-0.01050.7453-0.0846-0.10120.58680.05890.69915.8043-26.093547.8214
183.60760.8381-0.63063.85320.29256.9784-0.0773-0.1214-0.37350.08790.2704-0.55570.7240.319-0.18560.76140.0135-0.04960.533-0.0940.844413.5678-38.43250.7304
193.55180.1257-0.13196.33492.62875.91480.1083-0.3686-0.1365-0.85240.5257-0.5491-0.22840.6854-0.42620.7089-0.0788-0.09440.495-0.06150.719813.4893-24.030950.0761
202.81790.9953-0.15892.5182-0.54637.42090.1087-0.27210.13470.2706-0.10510.2192-0.4039-0.511-0.16770.4994-0.0083-0.03410.5583-0.01790.60392.958-21.312258.4883
215.08981.3480.1734.0836-1.99064.5913-0.01110.0876-1.4635-0.04310.22890.07650.6068-0.0032-0.24070.82910.03130.14780.7021-0.07951.005813.0774-14.835325.0489
225.72910.06361.7146.831.10952.5548-0.0228-0.96240.66440.71830.14080.85390.1066-0.7999-0.01670.56430.04580.13290.63680.02470.69962.06941.677937.7497
236.3516-0.26263.33597.2092-3.39796.764-0.03640.6170.65710.16050.1888-0.5549-0.4653-0.1411-0.12650.71850.02540.21510.548-0.06190.76735.349118.246731.0753
244.8704-0.3087-1.55864.35230.27191.4396-0.0378-0.44110.64250.41240.1352-0.4241-0.21440.0961-0.13590.66610.05930.05190.6152-0.08410.860711.10115.480137.5299
258.3715-3.87630.09428.19740.69617.9370.23121.29670.359-1.2324-0.49541.5699-0.0804-1.3199-0.05490.9987-0.0976-0.33641.14360.06580.84220.8784-0.26714.1378
265.46551.5584-3.70684.40831.7295.47190.42260.72870.6974-0.2149-0.578-0.1484-0.9846-0.72940.03770.730.08990.15720.95030.03780.843411.31171.506618.3496
270.914-1.4583-0.13053.5434-3.54977.0826-0.2268-0.21140.00450.4695-0.1032-0.0288-0.3833-0.76630.1960.6509-0.14990.01450.4946-0.00040.67914.5564-9.661746.5661
282.63680.3631-3.13115.1987-0.44183.6323-0.25890.1394-0.43540.2942-0.02110.10480.47490.1520.29210.72340.09710.10810.635-0.00330.635434.7632-10.726112.0596
296.71980.00221.38512.426-2.59075.61010.18170.2898-0.4222-0.19150.49330.43270.2749-0.4213-1.02380.64850.01970.11160.58920.00240.802523.86031.26629.2678
305.90211.30251.52060.52980.7361.76460.04880.2635-0.15530.1317-0.0193-0.03920.16630.1458-0.0280.62250.16740.03610.4920.09670.609538.54744.986212.6077
312.7162-1.35040.15596.0520.21362.0413-0.20930.0140.2680.13930.1241-0.29070.06830.16820.06780.68540.0740.0730.710.14410.629948.332230.207613.2863
323.2802-2.21881.38813.3393-1.31841.0322-0.2524-0.34320.69340.81040.2045-0.3448-0.56650.06450.03810.89710.0850.01610.7623-0.00790.681653.640927.572621.7076
337.72373.7033-1.79121.6251-0.78620.22060.02180.30140.1054-0.2611-0.11840.27810.0192-0.1639-0.03310.68560.12220.05890.65760.06410.662336.542514.207812.3381
346.5635-1.23011.88465.77980.72183.8140.24430.63780.08890.1643-0.5289-1.22361.36031.3050.36650.5220.13420.03210.7786-0.0260.692874.44499.452544.9788
352.7020.6092-0.16563.82751.58232.87150.1170.2114-0.39960.0967-0.0360.03950.51990.0838-0.08150.78060.0674-0.10090.73670.04160.836270.72973.260236.5965
362.04620.3928-1.64622.01931.51768.90350.018-0.01530.37280.0348-0.1204-0.03130.20910.18330.04780.42330.04780.06150.5094-0.01610.756773.596515.842445.9348
376.7402-0.5019-0.72146.37831.15522.68030.5956-1.07370.61990.1217-0.3016-0.8862-0.65620.7188-0.28570.7396-0.18830.11450.7398-0.16880.938177.480833.872960.611
383.5874-3.60874.16537.8166-4.83018.77320.91530.37461.2763-0.8968-0.6686-0.577-0.82270.10760.38721.2715-0.02160.47060.8424-0.13971.510172.037547.005771.0444
393.23180.7452-2.02413.03740.34046.03130.1867-0.17910.1101-0.0197-0.0034-0.2596-0.79670.1282-0.16460.7887-0.03890.15510.6191-0.12170.978468.924934.630364.7071
403.40211.446-1.78482.2398-0.97095.91520.1308-0.35380.00940.17910.0661-0.56310.210.6146-0.19740.70530.0194-0.02630.8043-0.07640.95274.661823.734165.5486
413.6936-1.50063.21546.940.11529.3466-0.63280.14280.752-1.1221-0.4638-0.5808-0.53910.5271.18721.11210.10690.00640.65170.01880.901971.170928.669835.4721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 224 )
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 142 )
13X-RAY DIFFRACTION13chain 'B' and (resid 143 through 157 )
14X-RAY DIFFRACTION14chain 'B' and (resid 158 through 177 )
15X-RAY DIFFRACTION15chain 'B' and (resid 178 through 203 )
16X-RAY DIFFRACTION16chain 'B' and (resid 204 through 224 )
17X-RAY DIFFRACTION17chain 'C' and (resid 18 through 44 )
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 109 )
19X-RAY DIFFRACTION19chain 'C' and (resid 110 through 142 )
20X-RAY DIFFRACTION20chain 'C' and (resid 143 through 203 )
21X-RAY DIFFRACTION21chain 'C' and (resid 204 through 224 )
22X-RAY DIFFRACTION22chain 'D' and (resid 18 through 55 )
23X-RAY DIFFRACTION23chain 'D' and (resid 56 through 82 )
24X-RAY DIFFRACTION24chain 'D' and (resid 83 through 142 )
25X-RAY DIFFRACTION25chain 'D' and (resid 143 through 157 )
26X-RAY DIFFRACTION26chain 'D' and (resid 158 through 177 )
27X-RAY DIFFRACTION27chain 'D' and (resid 178 through 223 )
28X-RAY DIFFRACTION28chain 'E' and (resid 17 through 129 )
29X-RAY DIFFRACTION29chain 'E' and (resid 130 through 158 )
30X-RAY DIFFRACTION30chain 'E' and (resid 159 through 224 )
31X-RAY DIFFRACTION31chain 'F' and (resid 18 through 68 )
32X-RAY DIFFRACTION32chain 'F' and (resid 69 through 177 )
33X-RAY DIFFRACTION33chain 'F' and (resid 178 through 224 )
34X-RAY DIFFRACTION34chain 'G' and (resid 14 through 44 )
35X-RAY DIFFRACTION35chain 'G' and (resid 45 through 157 )
36X-RAY DIFFRACTION36chain 'G' and (resid 158 through 224 )
37X-RAY DIFFRACTION37chain 'H' and (resid 19 through 55 )
38X-RAY DIFFRACTION38chain 'H' and (resid 56 through 82 )
39X-RAY DIFFRACTION39chain 'H' and (resid 83 through 159 )
40X-RAY DIFFRACTION40chain 'H' and (resid 160 through 203 )
41X-RAY DIFFRACTION41chain 'H' and (resid 204 through 224 )

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