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- PDB-4s1w: Structure of a putative Glutamine--Fructose-6-Phosphate Aminotran... -

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Basic information

Entry
Database: PDB / ID: 4s1w
TitleStructure of a putative Glutamine--Fructose-6-Phosphate Aminotransferase from Staphylococcus aureus subsp. aureus Mu50
ComponentsGlutamine--fructose-6-phosphate aminotransferase [isomerizing]
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / Essential Enzymes
Function / homology
Function and homology information


carbohydrate derivative biosynthetic process / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / carbohydrate derivative binding
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsFilippova, E.V. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Structure of a putative Glutamine--Fructose-6-Phosphate Aminotransferase from Staphylococcus aureus subsp. aureus Mu50
Authors: Filippova, E.V. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
B: Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0624
Polymers78,8502
Non-polymers2122
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-3 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.245, 61.617, 104.690
Angle α, β, γ (deg.)90.00, 112.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-867-

HOH

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Components

#1: Protein Glutamine--fructose-6-phosphate aminotransferase [isomerizing] / D-fructose-6-phosphate amidotransferase / GFAT / Glucosamine-6-phosphate synthase / Hexosephosphate ...D-fructose-6-phosphate amidotransferase / GFAT / Glucosamine-6-phosphate synthase / Hexosephosphate aminotransferase / L-glutamine--D-fructose-6-phosphate amidotransferase


Mass: 39425.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: glmS, BN965_3160, BN966_160, BN967_17410, BN968_17600, ER16_10920
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: A0A060U032, UniProt: A0A0J9X200*PLUS, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES buffer, 25 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 79565 / Num. obs: 79565 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 40.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.981 / SU ML: 0.067 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19188 3965 5 %RANDOM
Rwork0.15966 ---
obs0.16129 75317 97.08 %-
all-75317 --
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: 34.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å22.03 Å2
2---0.75 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 14 542 5791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195403
X-RAY DIFFRACTIONr_bond_other_d0.0010.025285
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9737342
X-RAY DIFFRACTIONr_angle_other_deg0.89312161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08124.957234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03915909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7621526
X-RAY DIFFRACTIONr_chiral_restr0.1010.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
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_it1.6012.2482747
X-RAY DIFFRACTIONr_mcbond_other1.62.2472746
X-RAY DIFFRACTIONr_mcangle_it2.1083.3623439
X-RAY DIFFRACTIONr_mcangle_other2.1083.3633440
X-RAY DIFFRACTIONr_scbond_it2.782.6062656
X-RAY DIFFRACTIONr_scbond_other2.7792.6062656
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0843.7743904
X-RAY DIFFRACTIONr_long_range_B_refined6.52620.1596514
X-RAY DIFFRACTIONr_long_range_B_other6.52620.1656515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 261 -
Rwork0.205 5375 -
obs--93.76 %
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)
10.53060.0609-0.28220.27750.04520.73380.03940.04020.08460.0295-0.00740.07-0.068-0.071-0.03210.04070.0053-0.01180.0593-0.00770.049320.135258.613237.7144
21.72120.18-0.00450.6967-0.24692.36980.1129-0.20840.18250.0805-0.09780.0082-0.22870.1308-0.01510.0699-0.0097-0.01470.0526-0.03420.042529.042766.569941.2516
30.34810.0374-0.28690.4790.06751.01250.0167-0.0350.04830.07350.01670.0908-0.0644-0.1109-0.03340.0597-0.0019-0.01440.0733-0.01060.059319.425957.384142.5693
41.5598-1.68550.3288.048-1.30611.9304-0.0804-0.00540.0863-0.19610.14180.2648-0.1173-0.1803-0.06140.0355-0.0139-0.01830.0969-0.00540.04716.112153.105436.0983
51.0666-0.4161-0.27691.1269-0.63171.6345-0.08550.1197-0.1288-0.1744-0.01060.06770.3184-0.08120.09610.1388-0.0481-0.01780.0774-0.03350.059721.760838.873526.1321
61.7056-1.137-0.6043.86990.1920.7480.05820.28840.0352-0.1488-0.05710.0469-0.0298-0.0239-0.00110.0261-0.0131-0.01650.08920.02320.013947.268561.45660.9941
71.69740.6268-0.55190.72550.0291.45480.02940.21720.1491-0.06560.06220.0659-0.1022-0.1415-0.09160.07590.007-0.04260.07960.03970.055631.473163.77089.2668
81.9143-0.2425-0.92841.9369-0.51351.3844-0.045-0.1023-0.05360.0142-0.0987-0.1793-0.00280.27880.14380.02660.0033-0.0250.11190.00760.050954.269855.184114.1524
91.71090.0205-1.11391.7124-0.51222.1217-0.1257-0.1969-0.26740.0106-0.055-0.07610.13910.05630.18070.04040.0218-0.00830.08860.02970.071441.49548.33124.0181
100.75540.4329-0.58391.1456-0.06971.7584-0.0928-0.1327-0.15820.0736-0.0342-0.14430.08220.25560.1270.04890.0266-0.02230.13950.02710.097151.097550.703923.1776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A248 - 337
2X-RAY DIFFRACTION2A338 - 380
3X-RAY DIFFRACTION3A381 - 419
4X-RAY DIFFRACTION4A420 - 443
5X-RAY DIFFRACTION5A444 - 585
6X-RAY DIFFRACTION6B246 - 286
7X-RAY DIFFRACTION7B287 - 421
8X-RAY DIFFRACTION8B424 - 462
9X-RAY DIFFRACTION9B463 - 504
10X-RAY DIFFRACTION10B505 - 590

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