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- PDB-1jt9: Structure of the mutant F174A T form of the Glucosamine-6-Phospha... -

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Basic information

Entry
Database: PDB / ID: 1jt9
TitleStructure of the mutant F174A T form of the Glucosamine-6-Phosphate deaminase from E.coli
ComponentsGlucosamine-6-Phosphate deaminase
KeywordsHYDROLASE / ALLOSTERIC ENZYME / ENTROPIC EFFECTS / ALDOSE-KETOSE ISOMERASE / STRUCTURAL FLEXIBILITY
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 / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBustos-Jaimes, I. / Sosa-Peinado, A. / Rudino-Pinera, E. / Horjales, E. / Calcagno, M.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase.
Authors: Bustos-Jaimes, I. / Sosa-Peinado, A. / Rudino-Pinera, E. / Horjales, E. / Calcagno, M.L.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 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 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,7361
Polymers29,7361
Non-polymers00
Water5,711317
1
A: Glucosamine-6-Phosphate deaminase
x 6


Theoretical massNumber of molelcules
Total (without water)178,4176
Polymers178,4176
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 area8910 Å2
ΔGint-63 kcal/mol
Surface area57720 Å2
MethodPISA
2
A: Glucosamine-6-Phosphate deaminase

A: Glucosamine-6-Phosphate deaminase

A: Glucosamine-6-Phosphate deaminase


Theoretical massNumber of molelcules
Total (without water)89,2083
Polymers89,2083
Non-polymers00
Water543
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
MethodPQS
Unit cell
Length a, b, c (Å)127.617, 127.617, 139.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Glucosamine-6-Phosphate deaminase / GLUCOSAMINE-6-PHOSPHATE ISOMERASE


Mass: 29736.113 Da / Num. of mol.: 1 / Mutation: F174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P0A759, glucosamine-6-phosphate deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.9 Msodium acetate1reservoir
2100 mMHEPES1reservoirpH7.0
35 mMGlcNAc6P1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / % possible obs: 99 % / Redundancy: 3.4 % / Rsym value: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.334
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 41650 / % possible obs: 99 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 11.1

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Processing

Software
NameVersionClassification
CNSrefinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1cd5

1cd5


Resolution: 2.06→47.13 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 4203 10.091 %Random
Rwork0.204 ---
all-42054 --
obs-41650 98.9 %-
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å2-0.32 Å20 Å2
2--1.69 Å20 Å2
3----3.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.06→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 0 317 2252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.06→2.2 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.2694 755 -
Rwork0.2451 --
obs-7376 99.5 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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