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- PDB-1fsf: GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER, AT 1.... -

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Basic information

Entry
Database: PDB / ID: 1fsf
TitleGLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER, AT 1.9A RESOLUTION
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsISOMERASE / ALLOSTERIC ENZYME / ENTROPIC EFFECTS / ALDOSE-KETOSE ISOMERASE / ANISOTROPIC REFINEMENT
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate metabolic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsRudino-Pinera, E. / Morales-Arrieta, S. / Rojas-Trejo, S.P. / Horjales, E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase.
Authors: Rudino-Pinera, E. / Morales-Arrieta, S. / Rojas-Trejo, S.P. / Horjales, E.
#1: Journal: Structure / Year: 1995
Title: Structure and catalytic mechanism of glucosamine-6-phosphate deaminase from Escherichia coli at 2.1A resolution
Authors: Oliva, G. / Fontes, M.R.M. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E.
#2: Journal: Structure / Year: 1999
Title: The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3A resolution
Authors: Horjales, E. / Altamirano, M.M. / Calcagno, M.L. / Garratt, R.C. / Oliva, G.
History
DepositionSep 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)29,8121
Polymers29,8121
Non-polymers00
Water5,368298
1
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
x 6


Theoretical massNumber of molelcules
Total (without water)178,8736
Polymers178,8736
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area9070 Å2
ΔGint-61 kcal/mol
Surface area62450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.676, 126.676, 139.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
DetailsThe biological assembly is a hexamer constructed from monomers A by two-fold and then a three-fold

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Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE / E.C.5.3.1.10 / GLUCOSAMINE-6-PHOSPHATE DEAMINASE / GNPDA / GLCN6P DEAMINASE


Mass: 29812.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTZ18-R / Production host: Escherichia coli (E. coli) / References: UniProt: P0A759, EC: 5.3.1.10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 4.04 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: HEPES, sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
22.45 Msodium acetate1reservoir
3100 mMHEPES1reservoirpH6.8

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.782
DetectorType: MACSCIENCE DIP100S / Detector: IMAGE PLATE / Date: Jan 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 48346 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.325 / Num. unique all: 7806 / % possible all: 90.9
Reflection
*PLUS
Num. obs: 48346 / % possible obs: 93.1 %
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 91.2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
CCP4data scaling
CNSphasing
RefinementResolution: 1.9→50 Å / Num. parameters: 21513 / Num. restraintsaints: 25995 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: FIRST REFINED WITH A CNS ISOTROPIC REFINEMENT AND THEN BY SHELXL ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4880 10 %RANDOM
Rwork0.183 ---
all-48346 --
obs-48346 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5571 Å2 / ksol: 0.370572 e/Å3
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2390
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 298 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_mcbond_it0.931.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 765 9.8 %
Rwork0.274 7041 -
obs-7041 90.9 %
Software
*PLUS
Name: 'CNS, SHELXL' / Version: '0.5, 97' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it0.931.5
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.274 / Rfactor obs: 0.274

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