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- PDB-3ge1: 2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Sta... -

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Basic information

Entry
Database: PDB / ID: 3ge1
Title2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol
ComponentsGlycerol kinase
KeywordsTRANSFERASE / Glycerol Kinase / Glycerol / ADP / idp00743 / ATP-binding / Glycerol metabolism / Kinase / Nucleotide-binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / ATP binding / cytosol
Similarity search - Function
Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Glycerol kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMinasov, G. / Brunzelle, J. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol
Authors: Minasov, G. / Brunzelle, J. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol kinase
B: Glycerol kinase
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,86424
Polymers225,8864
Non-polymers2,97920
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17040 Å2
ΔGint-176 kcal/mol
Surface area63710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.412, 193.651, 91.844
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 2 - 497 / Label seq-ID: 5 - 500

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2
DetailsChains A, B, C, D represent biological assembly (tetramer).

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycerol kinase / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 56471.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: Staphylococcus aureus subsp. aureus COL / Gene: glpK, SACOL1320 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q5HGD2, glycerol kinase

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Non-polymers , 5 types, 294 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 2% Glycerol, PEG3350 20%, 0.2M Sodium dihydrogen Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97624
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2008 / Details: BERYLLIUM LENSES
RadiationMonochromator: SI{111} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 56438 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 18.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.6 / % possible all: 83.1

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZW

3ezw


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 37.063 / SU ML: 0.322 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Atomic Temperature Factors were Refined
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2855 5.1 %RANDOM
Rwork0.191 ---
obs0.194 53455 96.8 %-
all-53455 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.81 Å2
Baniso -1Baniso -2Baniso -3
1-12.01 Å2-0 Å22.84 Å2
2---6.79 Å2-0 Å2
3----3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15660 0 176 274 16110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216169
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210770
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.94821913
X-RAY DIFFRACTIONr_angle_other_deg0.691326219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.27351990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.65324.812771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.141152740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6841584
X-RAY DIFFRACTIONr_chiral_restr0.0660.22376
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023314
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8481.59827
X-RAY DIFFRACTIONr_mcbond_other0.2471.54112
X-RAY DIFFRACTIONr_mcangle_it1.593215770
X-RAY DIFFRACTIONr_scbond_it2.86236342
X-RAY DIFFRACTIONr_scangle_it4.5164.56143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2909tight positional0.070.1
22B2914tight positional0.060.1
11A3634medium positional0.132
22B3640medium positional0.122
11A2909tight thermal0.462
22B2914tight thermal0.472
11A3634medium thermal0.535
22B3640medium thermal0.575
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 193 -
Rwork0.321 3193 -
obs--79.02 %
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)
19.46494.5970.0324.766-0.21881.0038-0.1827-0.4475-0.1378-0.68680.01610.409-0.0404-0.41790.16660.1606-0.0319-0.11860.2848-0.0730.1541-22.7695-56.86810.3111
21.3690.48620.05492.1493-0.63381.2353-0.11390.1153-0.2374-0.2112-0.0344-0.24470.24920.17310.14820.0660.02210.0460.1387-0.06730.1362-4.1766-50.7619-10.1259
31.21760.0562-0.99611.8291-0.4242.6856-0.11850.3179-0.254-0.6740.0060.09890.2242-0.35270.11250.2906-0.0544-0.04730.2-0.12460.1739-15.6807-53.5053-18.6407
41.58640.64230.29243.32622.34152.6088-0.0059-0.0893-0.03070.1915-0.05560.23090.4053-0.39030.06150.1114-0.081-0.05440.16310.01030.0962-17.777-30.5601-2.2746
53.04241.62270.11933.14821.61792.7812-0.09480.0436-0.0278-0.6777-0.24210.6126-0.1022-0.58270.33690.23790.0019-0.18670.24-0.02080.187-23.1847-29.0264-7.6579
60.3984-1.2854-0.10419.13880.82260.0877-0.04640.12950.0253-0.2435-0.03320.5126-0.0066-0.04850.07950.1098-0.1119-0.05030.2827-0.06050.1573-30.8237-48.8215-9.4661
72.38431.30040.73434.1924-0.32671.1315-0.1420.37110.1201-0.38270.16180.7938-0.0619-0.3728-0.01990.09110.0471-0.12310.3953-0.0650.208-26.4856-28.449-11.2825
84.21070.98292.75653.47571.35835.94010.386-0.39720.1759-0.0209-0.177-0.08490.27870.0453-0.2090.0514-0.0377-0.01770.1185-0.01870.1327-11.87252.589724.0557
92.7304-0.44390.59921.35670.2091.82240.2780.30880.1374-0.76080.0420.1762-0.5714-0.2095-0.320.56440.0669-0.00130.1020.09320.1988-18.46617.88716.9253
100.9723-0.0999-0.30721.59751.1320.99330.10380.17270.3429-0.9464-0.0490.1487-0.6479-0.1741-0.05480.58140.0392-0.09660.15480.09440.2501-17.570813.41194.7323
111.40010.09210.08352.15040.85981.68950.08160.03980.3999-0.86770.1523-0.3268-0.69390.3264-0.23390.4848-0.12220.14260.0993-0.03440.2775-5.185313.35849.577
121.98690.9113-0.34985.78520.43933.34080.1106-0.3075-0.0805-0.32070.0668-0.3694-0.09520.0261-0.17740.0412-0.0227-0.0040.1061-0.03690.1028-6.5082-17.1584.9573
131.6713-1.89161.39424.0138-0.02932.58390.06350.10910.1894-0.45670.1374-0.746-0.36180.4881-0.2010.1418-0.14390.04110.3856-0.10090.41577.3704-5.7927.8958
141.03780.35660.09262.13270.89222.74130.0978-0.0965-0.0124-0.65210.3352-0.8568-0.34080.5783-0.4330.2701-0.14690.24760.23-0.14440.43185.0081-3.4248.7246
155.3953-0.3584-1.93593.08290.55973.9290.40530.2053-0.105-0.4333-0.1549-0.4182-0.150.1793-0.25030.08620.03230.03460.08150.06520.1871-7.4055-58.421118.1376
166.32440.3162-1.91652.25341.87144.48510.11130.1592-0.1712-0.37230.0453-0.16530.527-0.0596-0.15660.4315-0.00990.01090.04010.08280.2383-11.4335-68.022518.5757
170.9235-0.7854-0.26722.59030.6821.1955-0.0843-0.1808-0.29190.42710.03870.18480.4511-0.25560.04560.1972-0.092-0.01620.18830.10210.2172-20.3432-69.773734.3559
180.95630.0328-0.61842.25050.14721.1015-0.0195-0.29-0.21560.04590.0551-0.34220.28350.3378-0.03560.10550.0738-0.06580.24420.06510.2893-3.9662-68.538731.6329
192.0955-2.0799-0.16286.68490.34070.62340.22780.00410.0957-0.5744-0.0404-0.36520.04390.1665-0.18740.06220.00430.00220.2630.03640.0984-11.7045-41.497436.6692
201.1693-1.5971-1.13365.49574.38133.53240.0049-0.31980.01890.2940.3986-0.5290.260.338-0.40350.03620.0553-0.04270.50360.08890.43265.3332-54.457835.2615
217.6306-2.5757-3.11371.68640.41953.6642-0.2218-1.14660.440.31490.23-0.45560.08240.6545-0.00820.09490.0077-0.09840.38450.08740.2067-8.0027-40.669248.8466
224.3846-1.84141.95523.4886-1.64484.66060.22490.17670.3266-0.2278-0.27760.36110.0011-0.0180.05280.02510.0131-0.01190.2396-0.07020.1464-27.0919-3.256634.2921
230.99110.1179-0.11321.44230.32791.56290.016-0.18850.0680.48450.0219-0.0375-0.11220.2968-0.03790.1993-0.0404-0.01620.324-0.06060.0822-21.4165-6.770954.062
241.0938-0.0621-0.21422.464-0.31781.46040.0396-0.11230.16140.3750.0430.5213-0.1637-0.2985-0.08260.07180.0110.07170.3094-0.06050.2303-35.8303-5.402352.0656
253.313-0.5226-0.21540.8096-0.92732.35450.18970.31950.1692-0.5409-0.17620.09580.4360.037-0.01360.42140.0945-0.11050.2423-0.00250.1239-25.8273-26.524431.0137
262.9173-1.91480.14045.2074-1.05862.8966-0.1456-0.1106-0.0958-0.2866-0.0810.77810.2665-0.32730.22670.0649-0.049-0.050.2826-0.01120.216-32.5936-30.162141.6126
270.1702-0.6626-0.02143.5394-0.00312.14760.09620.0586-0.0029-0.5442-0.05150.67060.092-0.4547-0.04470.0892-0.016-0.1290.4596-0.02510.5153-44.5858-12.719935.0272
284.9346-4.06872.60823.461-2.69574.5320.0647-0.2432-1.0339-0.18710.22270.8420.7262-0.4936-0.28740.1635-0.11730.01920.3062-0.03130.3573-35.9797-37.089942.9379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 35
2X-RAY DIFFRACTION2A36 - 178
3X-RAY DIFFRACTION3A179 - 300
4X-RAY DIFFRACTION4A301 - 357
5X-RAY DIFFRACTION5A358 - 417
6X-RAY DIFFRACTION6A418 - 458
7X-RAY DIFFRACTION7A459 - 498
8X-RAY DIFFRACTION8B0 - 70
9X-RAY DIFFRACTION9B71 - 120
10X-RAY DIFFRACTION10B121 - 195
11X-RAY DIFFRACTION11B196 - 305
12X-RAY DIFFRACTION12B306 - 386
13X-RAY DIFFRACTION13B387 - 436
14X-RAY DIFFRACTION14B437 - 497
15X-RAY DIFFRACTION15C1 - 66
16X-RAY DIFFRACTION16C67 - 96
17X-RAY DIFFRACTION17C97 - 206
18X-RAY DIFFRACTION18C207 - 296
19X-RAY DIFFRACTION19C297 - 387
20X-RAY DIFFRACTION20C388 - 468
21X-RAY DIFFRACTION21C469 - 497
22X-RAY DIFFRACTION22D2 - 70
23X-RAY DIFFRACTION23D71 - 178
24X-RAY DIFFRACTION24D179 - 303
25X-RAY DIFFRACTION25D304 - 338
26X-RAY DIFFRACTION26D339 - 412
27X-RAY DIFFRACTION27D413 - 468
28X-RAY DIFFRACTION28D469 - 497

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