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- PDB-1fqo: GLUCOSAMINE 6-PHOSPHATE DEAMINASE COMPLEXED WITH THE SUBSTRATE OF... -

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Basic information

Entry
Database: PDB / ID: 1fqo
TitleGLUCOSAMINE 6-PHOSPHATE DEAMINASE COMPLEXED WITH THE SUBSTRATE OF THE REVERSE REACTION FRUCTOSE 6-PHOSPHATE (OPEN FORM)
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsISOMERASE / ALLOSTERIC ENZYME / ENTROPIC EFFECTS / ALDOSE-KETOSE ISOMERASE
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 / cytoplasm / cytosol
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
FRUCTOSE -6-PHOSPHATE / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 6, 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 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4May 9, 2012Group: Non-polymer description
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6656
Polymers59,6242
Non-polymers1,0414
Water5,495305
1
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules

A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules

A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,99518
Polymers178,8736
Non-polymers3,12212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16820 Å2
ΔGint-107 kcal/mol
Surface area61220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.040, 126.040, 223.508
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingrhombohedral
Space group name H-MH32
DetailsThe biological assembly is an hexamer which can be constructed from chain A and B by the tree-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.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH FRUCTOSE-6-PHOSPHATE IN BOTH ACTIVE AND ALLOSTERIC SITES
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: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium acetate, HEPES, fructose 6-phosphate, pH 7.5, 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
22.8 Msodium acetate1reservoir
3100 mMHEPES1reservoirpH7.5
427 mMFru6P1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 35080 / % possible obs: 94.6 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.182 / Num. unique all: 2496 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.15 Å / Num. obs: 35080
Reflection shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.2 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MAR345data collection
DENZOdata reduction
CCP4data reduction
X-PLORmodel building
X-PLOR3.851refinement
CCP4data scaling
X-PLORphasing
RefinementResolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3508 10 %RANDOM
Rwork0.187 ---
all-35080 --
obs--94.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 64 305 4553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.5
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.5

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