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- PDB-7dnr: Crystal Structure of Zn-bound SIS Domain of Glucosamine-6-P Synth... -

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Basic information

Entry
Database: PDB / ID: 7dnr
TitleCrystal Structure of Zn-bound SIS Domain of Glucosamine-6-P Synthase from E. coli
ComponentsGlutamine--fructose-6-phosphate aminotransferase [isomerizing]
KeywordsISOMERASE / Metal binding / Zinc ion
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGao, C. / Xiao, J.
CitationJournal: To Be Published
Title: Discovery of Metal-binding Proteins by Thermal Proteome Profiling
Authors: Zeng, X. / Wei, T. / Liu, Y. / Wang, X. / Feng, T. / Cheng, Y. / Qin, W. / Gao, C. / Xiao, J. / Wang, C.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)80,9105
Polymers80,7142
Non-polymers1963
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-127 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.099, 67.889, 73.952
Angle α, β, γ (deg.)90.000, 111.440, 90.000
Int Tables number4
Space group name H-MP1211

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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: 40357.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: glmS, b3729, JW3707 / Production host: Escherichia coli (E. coli)
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 5000 MME, sodium acetate, zinc cloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 85139 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Χ2: 0.609 / Net I/σ(I): 7.5 / Num. measured all: 577746
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.636.60.69442600.8590.2890.7530.423100
1.63-1.666.60.62442220.880.2610.6780.43100
1.66-1.696.50.5241990.9130.2210.5660.434100
1.69-1.726.90.45342500.9420.1850.490.425100
1.72-1.766.90.40842600.9490.1660.4410.448100
1.76-1.86.90.31842300.9660.1290.3440.45100
1.8-1.856.80.25242500.9780.1030.2730.459100
1.85-1.96.60.20742400.9830.0870.2250.464100
1.9-1.956.70.15842460.990.0650.1710.486100
1.95-2.0270.12742300.9930.0520.1380.505100
2.02-2.0970.10342580.9950.0420.1120.531100
2.09-2.176.90.08542620.9960.0350.0920.561100
2.17-2.276.50.07242350.9970.030.0780.591100
2.27-2.396.90.06142690.9980.0250.0660.619100
2.39-2.5470.05542300.9980.0220.0590.671100
2.54-2.746.80.04942730.9980.020.0530.735100
2.74-3.016.70.04342750.9990.0180.0460.82599.9
3.01-3.457.10.03742640.9990.0150.0390.951100
3.45-4.346.70.03243180.9990.0130.0341.12100
4.34-506.50.03143680.9990.0130.0331.0399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.43 Å32.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOQ

1moq


Resolution: 1.7→23.52 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1667 2.35 %
Rwork0.2145 69410 -
obs0.2149 71077 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.47 Å2 / Biso mean: 27.8161 Å2 / Biso min: 11.91 Å2
Refinement stepCycle: final / Resolution: 1.7→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 3 489 5976
Biso mean--19.28 32.73 -
Num. residues----711
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.750.29331340.296257535887
1.75-1.810.29121420.282257635905
1.81-1.870.25321420.272757165858
1.87-1.950.2911370.276157905927
1.95-2.030.30381360.265657695905
2.03-2.140.29211460.244257375883
2.14-2.280.281370.249257845921
2.28-2.450.24341400.246157735913
2.45-2.70.22751350.233257975932
2.7-3.090.25531380.212758015939
3.09-3.890.20791390.179258265965
3.89-23.520.19121410.174759016042

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