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- PDB-1cd5: GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER -

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Basic information

Entry
Database: PDB / ID: 1cd5
TitleGLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER
ComponentsPROTEIN (GLUCOSAMINE 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
Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHorjales, E. / Altamirano, M.M. / Calcagno, M.L. / Garratt, R.C. / Oliva, G.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution.
Authors: Horjales, E. / Altamirano, M.M. / Calcagno, M.L. / Garratt, R.C. / Oliva, G.
History
DepositionMar 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE)


Theoretical massNumber of molelcules
Total (without water)29,8121
Polymers29,8121
Non-polymers00
Water2,540141
1
A: PROTEIN (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
Unit cell
Length a, b, c (Å)129.810, 129.810, 139.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322

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Components

#1: Protein PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE) / E.C.5.3.1.10


Mass: 29812.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAS THIS STRUCTURE PRESENTS THE ENZYME WITHOUT LIGANDS IT CORRESPOND TO THE T-CONFORMER OF THIS ...AS THIS STRUCTURE PRESENTS THE ENZYME WITHOUT LIGANDS IT CORRESPOND TO THE T-CONFORMER OF THIS ALLOSTERIC ENZYME.

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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 % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: sodium acetate, hepes, pH 7.0, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2hepes11
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21.75 Msodium acetate1reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorDate: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 30597 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.6 / Rsym value: 34 / % possible all: 98
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DEA

1dea


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3829 10 %RANDOM
Rwork0.207 ---
obs-29545 95.3 %-
Displacement parametersBiso mean: 41.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 141 2233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.35 392 10 %
Rwork0.318 3366 -
obs--95.3 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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