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- PDB-6wct: Crystal structure of a guanylate kinase from Stenotrophomonas mal... -

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Basic information

Entry
Database: PDB / ID: 6wct
TitleCrystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate
ComponentsGuanylate kinase
KeywordsTRANSFERASE / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / gram-negative bacterium / multi-drug resistant / kinase / ATP / GMP / ADP / GDP / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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. ...Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Guanylate kinase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D.
History
DepositionMar 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,46010
Polymers100,8504
Non-polymers1,6106
Water5,152286
1
A: Guanylate kinase
C: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2465
Polymers50,4252
Non-polymers8213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-38 kcal/mol
Surface area18160 Å2
MethodPISA
2
B: Guanylate kinase
D: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2135
Polymers50,4252
Non-polymers7893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.660, 101.420, 70.020
Angle α, β, γ (deg.)90.000, 92.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 12 through 39 or (resid 40...
21(chain B and (resid 12 through 120 or (resid 121...
31(chain C and (resid 12 through 39 or (resid 40...
41(chain D and (resid 12 through 39 or (resid 40...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPRO(chain A and (resid 12 through 39 or (resid 40...AA12 - 3920 - 47
12GLNGLNGLNGLN(chain A and (resid 12 through 39 or (resid 40...AA4048
13ALAALA5GP5GP(chain A and (resid 12 through 39 or (resid 40...AA - E12 - 30120
14ALAALA5GP5GP(chain A and (resid 12 through 39 or (resid 40...AA - E12 - 30120
15ALAALA5GP5GP(chain A and (resid 12 through 39 or (resid 40...AA - E12 - 30120
16ALAALA5GP5GP(chain A and (resid 12 through 39 or (resid 40...AA - E12 - 30120
21ALAALAARGARG(chain B and (resid 12 through 120 or (resid 121...BB12 - 12020 - 128
22GLNGLNGLNGLN(chain B and (resid 12 through 120 or (resid 121...BB121129
23VALVAL5GP5GP(chain B and (resid 12 through 120 or (resid 121...BB - G11 - 30119
24VALVAL5GP5GP(chain B and (resid 12 through 120 or (resid 121...BB - G11 - 30119
25VALVAL5GP5GP(chain B and (resid 12 through 120 or (resid 121...BB - G11 - 30119
26VALVAL5GP5GP(chain B and (resid 12 through 120 or (resid 121...BB - G11 - 30119
31ALAALAPROPRO(chain C and (resid 12 through 39 or (resid 40...CC12 - 3920 - 47
32GLNGLNGLNGLN(chain C and (resid 12 through 39 or (resid 40...CC4048
33ALAALA5GP5GP(chain C and (resid 12 through 39 or (resid 40...CC - H12 - 30120
34ALAALA5GP5GP(chain C and (resid 12 through 39 or (resid 40...CC - H12 - 30120
35ALAALA5GP5GP(chain C and (resid 12 through 39 or (resid 40...CC - H12 - 30120
36ALAALA5GP5GP(chain C and (resid 12 through 39 or (resid 40...CC - H12 - 30120
41ALAALAPROPRO(chain D and (resid 12 through 39 or (resid 40...DD12 - 3920 - 47
42GLNGLNGLNGLN(chain D and (resid 12 through 39 or (resid 40...DD4048
43ALAALA5GP5GP(chain D and (resid 12 through 39 or (resid 40...DD - I10 - 30118
44ALAALA5GP5GP(chain D and (resid 12 through 39 or (resid 40...DD - I10 - 30118
45ALAALA5GP5GP(chain D and (resid 12 through 39 or (resid 40...DD - I10 - 30118
46ALAALA5GP5GP(chain D and (resid 12 through 39 or (resid 40...DD - I10 - 30118

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Components

#1: Protein
Guanylate kinase / GMP kinase


Mass: 25212.443 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: gmk, Smlt3842 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FT06, guanylate kinase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 33 mg/mL StmaA.01463.a.B1.PW38755 in 7 mM magnesium chloride, 7 mM ATP, 7 mM GMP (5GP) against MCSG1 screen condition B1 (0.6 M sodium chloride, 0.1 M MES, pH 6.5, 20% PEG4000), supplemented ...Details: 33 mg/mL StmaA.01463.a.B1.PW38755 in 7 mM magnesium chloride, 7 mM ATP, 7 mM GMP (5GP) against MCSG1 screen condition B1 (0.6 M sodium chloride, 0.1 M MES, pH 6.5, 20% PEG4000), supplemented with 20% ethylene glycol as cryoprotectant, unique puck ID pfi1-7, crystal tracking ID 314557b1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 19, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→47.51 Å / Num. obs: 51005 / % possible obs: 99.9 % / Redundancy: 4.665 % / Biso Wilson estimate: 48.413 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.05 / Χ2: 1.013 / Net I/σ(I): 18.97 / Num. measured all: 237940 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.154.6880.5782.9817625376037600.9030.652100
2.15-2.214.6820.4713.5517142366336610.9270.53199.9
2.21-2.284.670.4064.0216622356135590.9510.45899.9
2.28-2.354.6920.3194.9916214345734560.9640.36100
2.35-2.424.7020.2526.2615882337833780.9790.284100
2.42-2.514.6950.1857.8115293326132570.9890.20999.9
2.51-2.64.7070.1639.0514758313631350.9880.184100
2.6-2.714.6970.12811.3514129301130080.9920.14599.9
2.71-2.834.6960.09714.2613596289528950.9950.109100
2.83-2.974.6880.07218.6313033278327800.9970.08199.9
2.97-3.134.6790.05623.6512259262226200.9980.06399.9
3.13-3.324.6580.04528.511677251025070.9980.0599.9
3.32-3.554.6280.03634.3210849234623440.9990.04199.9
3.55-3.834.6560.03139.0910141218221780.9990.03599.8
3.83-4.24.6090.02745.039305202520190.9990.03199.7
4.2-4.74.6120.02448.488366181518140.9990.02799.9
4.7-5.424.6010.02448.127486162716270.9990.027100
5.42-6.644.5810.02448.466198135613530.9990.02799.8
6.64-9.394.5410.02152.234850106910680.9990.02499.9
9.39-47.514.2920.02154.4625156045860.9990.02497

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix1.17.1-3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TR0

3tr0


Resolution: 2.1→47.51 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 2890 6.04 %
Rwork0.1792 44956 -
obs0.1822 47846 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.13 Å2 / Biso mean: 57.0784 Å2 / Biso min: 22.09 Å2
Refinement stepCycle: final / Resolution: 2.1→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 105 286 6516
Biso mean--55.23 52.45 -
Num. residues----808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3528X-RAY DIFFRACTION9.226TORSIONAL
12B3528X-RAY DIFFRACTION9.226TORSIONAL
13C3528X-RAY DIFFRACTION9.226TORSIONAL
14D3528X-RAY DIFFRACTION9.226TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.36861200.3071851197182
2.13-2.170.3471010.29031926202783
2.17-2.210.33831240.281944206885
2.21-2.250.34041310.26911976210786
2.25-2.30.30451370.2581937207488
2.3-2.350.30511370.24022029216689
2.35-2.40.32211420.22782077221990
2.4-2.460.27281440.22882064220892
2.46-2.530.28781170.22162165228294
2.53-2.60.32941250.2282184230995
2.61-2.690.29391440.2172144228895
2.69-2.790.25211400.20952192233296
2.79-2.90.24081440.20992239238398
2.9-3.030.24711480.19682219236798
3.03-3.190.2651490.19272283243299
3.19-3.390.23321590.19022241240099
3.39-3.650.2141410.17912277241899
3.65-4.020.20811510.149422762427100
4.02-4.60.18461590.125522852444100
4.6-5.790.17921450.142523132458100
5.79-47.510.18251320.15122334246699
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)
11.04260.66681.06655.43033.32935.5455-0.0912-0.0760.18310.5183-0.44520.7171-0.0512-0.45580.40750.3144-0.06630.0710.2874-0.0590.50942.48115.311836.7791
22.7847-0.70020.90460.2667-0.99886.88250.0541.0770.46120.02720.3225-1.0645-0.81121.5093-0.30910.4884-0.1147-0.10051.03650.09340.895322.5571-2.935536.8792
31.01590.02451.46393.61860.23755.2448-0.179-0.04320.1192-0.0718-0.0974-0.0569-0.3544-0.07880.25580.246-0.0598-0.00090.2517-0.03340.37572.1297-0.214922.973
45.4924-5.7126-5.09256.78465.09474.7688-0.2797-0.71860.77040.29450.6025-0.00890.0534-0.4548-0.42350.45770.0957-0.00490.917-0.03820.477529.4623-12.3297.9347
52.53461.5006-0.91781.94-0.91580.46560.099-0.6424-0.4908-0.0913-0.06720.60450.4114-0.95660.40150.146-0.73970.0971.63320.21660.515425.5176-26.02552.3985
60.2523-0.2728-0.68243.8589-1.77334.1341-0.2618-0.8561-0.3178-0.0532-0.0190.62460.0418-1.7134-0.44620.3798-0.10920.00591.1970.05180.618920.1001-15.8995-3.7433
72.88080.5628-3.49042.6333-1.56198.1778-0.4784-0.4795-0.8391-0.26140.17942.16390.6969-2.2824-0.06540.5325-0.1336-0.15141.24920.09520.945315.3696-16.3877-9.6658
87.9765-2.35970.25886.1687-1.38328.6464-0.65190.10640.5217-0.1914-0.07930.4083-0.6456-0.58150.5550.60170.0379-0.28960.62770.02220.462624.9374-5.4179-11.2859
95.2758-1.0829-2.60653.37781.64885.6978-0.5416-0.69720.38110.23770.1350.479-0.7228-0.88670.45580.44780.2104-0.10520.92840.00870.480724.5757-9.29040.7908
105.3111-2.13421.50072.6833-2.1597.7204-0.5758-0.30040.5232-0.0150.129-0.0427-0.5476-0.66930.32420.3051-0.0126-0.07320.45970.01630.33335.8264-13.2762-0.2514
112.4442-2.7052.88044.895-4.06826.66210.47950.2199-0.9762-0.33760.73620.44051.5629-1.3748-0.07361.1004-0.5029-0.05870.5953-0.00660.545132.9593-34.568-9.7292
122.9417-0.1326-0.30552.80.71372.3711-0.0333-0.0685-0.2695-0.17870.10940.1150.6304-1.4027-0.00980.3586-0.1897-0.01680.63560.05780.379434.8309-24.40460.5368
135.42823.09544.99722.23922.61784.7099-0.2144-0.6030.816-0.4324-0.56260.6923-1.1881-1.37490.77730.57130.2575-0.03480.5563-0.02230.489334.3931-6.89126.7909
148.9562-2.80922.31186.08611.78386.8554-0.22510.5460.5252-0.4269-0.0884-0.2525-0.86130.57320.36990.4981-0.1578-0.04120.53240.03580.3103-0.5927-1.82911.3871
155.32730.58360.9213.21170.47984.672-0.35450.65370.4374-0.54490.0551-0.4311-0.24360.82330.38390.4207-0.10950.08550.48670.05210.4124-6.4761-12.3379-10.5734
165.48911.79314.17175.22941.62979.2414-0.03020.3844-0.45410.34810.3775-0.59540.40550.7520.19530.3196-0.03540.07280.3629-0.04550.4808-4.1905-16.3456-3.0695
175.48222.21112.81665.38552.91056.5461-0.0710.01260.41470.3228-0.58520.2719-0.2596-0.00420.49070.3354-0.097-0.02030.37610.00790.3066-7.5276-8.07644.1146
183.97222.00910.75836.46650.90082.0523-0.2560.41031.2847-0.9184-0.33920.4887-0.6677-0.61340.4810.76530.1254-0.26290.8752-0.00360.935-17.10966.6664-4.3531
194.33250.52781.89872.1494-0.03974.9386-0.15770.3080.1352-0.42670.0499-0.1278-0.09440.30050.17460.2195-0.0430.02250.2633-0.05320.30963.6052-4.372715.3591
203.8475-0.5460.27648.40031.22250.22250.1417-0.15620.01450.5239-0.06820.1690.4587-0.1105-0.10720.5488-0.1221-0.10260.5060.18890.409942.7434-25.663225.5868
211.82760.2196-0.14243.6133-0.8883.0480.14030.0132-0.06770.354-0.04680.03310.1588-0.0115-0.08680.39410.0294-0.01310.22340.02090.4457.5796-25.45635.2722
224.4241.2361.25056.94031.49832.68330.16850.36240.2186-0.47510.1280.26650.327-0.3594-0.42010.4591-0.0324-0.01180.30410.08790.36255.1663-25.60225.6103
237.16050.095-0.083.13742.42496.5705-0.03960.34760.74290.15360.0778-0.074-0.0777-0.4712-0.11570.41520.0024-0.00440.28020.12570.341147.7745-15.124825.1475
242.04441.0458-3.12222.9906-4.53258.18310.0238-0.16760.13370.0367-0.1872-0.3220.5431-0.8346-0.03290.6422-0.0757-0.05310.677-0.03890.434639.0622-14.250841.213
251.310.64151.44352.5306-0.46661.98720.0479-0.2834-0.25090.1453-0.05450.21420.389-0.6232-0.00860.2536-0.08370.02610.40260.04040.318239.8468-24.32712.2832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 135 )A12 - 135
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 150 )A136 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 215 )A151 - 215
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 21 )B11 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 37 )B22 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 53 )B38 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 66 )B54 - 66
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 87 )B67 - 87
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 112 )B88 - 112
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 133 )B113 - 133
11X-RAY DIFFRACTION11chain 'B' and (resid 134 through 151 )B134 - 151
12X-RAY DIFFRACTION12chain 'B' and (resid 152 through 196 )B152 - 196
13X-RAY DIFFRACTION13chain 'B' and (resid 197 through 215 )B197 - 215
14X-RAY DIFFRACTION14chain 'C' and (resid 12 through 37 )C12 - 37
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 87 )C38 - 87
16X-RAY DIFFRACTION16chain 'C' and (resid 88 through 102 )C88 - 102
17X-RAY DIFFRACTION17chain 'C' and (resid 103 through 133 )C103 - 133
18X-RAY DIFFRACTION18chain 'C' and (resid 134 through 170 )C134 - 170
19X-RAY DIFFRACTION19chain 'C' and (resid 171 through 216 )C171 - 216
20X-RAY DIFFRACTION20chain 'D' and (resid 10 through 37 )D10 - 37
21X-RAY DIFFRACTION21chain 'D' and (resid 38 through 87 )D38 - 87
22X-RAY DIFFRACTION22chain 'D' and (resid 88 through 112 )D88 - 112
23X-RAY DIFFRACTION23chain 'D' and (resid 113 through 135 )D113 - 135
24X-RAY DIFFRACTION24chain 'D' and (resid 136 through 170 )D136 - 170
25X-RAY DIFFRACTION25chain 'D' and (resid 171 through 216 )D171 - 216

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