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- PDB-1frz: GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPL... -

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Basic information

Entry
Database: PDB / ID: 1frz
TitleGLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION
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 / 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
Chem-16G / 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 7, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)60,2274
Polymers59,6242
Non-polymers6022
Water4,234235
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)180,68012
Polymers178,8736
Non-polymers1,8076
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 area14100 Å2
ΔGint-71 kcal/mol
Surface area61830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.720, 125.720, 223.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingrhombohedral
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2606-

HOH

DetailsThe biological assembly is a hexamer constructed from monomers A and B generated by the 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.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / 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: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, sodium acetate, 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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 30845 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.77
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.305 / Num. unique all: 3846 / % possible all: 74.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 31426 / % possible obs: 90.5 %
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.25 Å / % possible obs: 72.3 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
DENZOdata reduction
CCP4data scaling
CNSphasing
RefinementResolution: 2.2→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3087 10 %RANDOM
Rwork0.199 ---
all-30845 --
obs--89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.2007 Å2 / ksol: 0.400966 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.48 Å20.48 Å20 Å2
2---1.48 Å20 Å2
3---2.96 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 38 235 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 437 10.2 %
Rwork0.239 3846 -
obs-4283 74.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.228
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_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.282 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.239

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