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- PDB-1dea: STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAM... -

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Basic information

Entry
Database: PDB / ID: 1dea
TitleSTRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION
ComponentsGLUCOSAMINE 6-PHOSPHATE DEAMINASE
KeywordsINTRAMOLECULAR OXIDOREDUCTASE DEAMINASE
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
PHOSPHATE ION / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsOliva, G. / Fontes, M.R.M. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E.
Citation
Journal: Structure / Year: 1995
Title: Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution.
Authors: Oliva, G. / Fontes, M.R. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Crystallographic Studies of Glucosamine-6-Phosphate Deaminase from Escherichia Coli K12
Authors: Horjales, E. / Altamirano, M.M. / Calcagno, M.L. / Dauter, Z. / Wilson, K. / Garratt, R.C. / Oliva, G.
History
DepositionSep 13, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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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)60,0046
Polymers59,6242
Non-polymers3804
Water6,269348
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)180,01318
Polymers178,8736
Non-polymers1,14012
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 area13580 Å2
ΔGint-138 kcal/mol
Surface area61440 Å2
MethodPISA
2
A: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules

A: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules

A: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0069
Polymers89,4373
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
3
B: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules

B: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules

B: GLUCOSAMINE 6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0069
Polymers89,4373
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.710, 125.710, 222.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein GLUCOSAMINE 6-PHOSPHATE DEAMINASE


Mass: 29812.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A759, EC: 5.3.1.10
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.33 M / Common name: sodium potassium phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 38368 / % possible obs: 97.4 % / Rmerge(I) obs: 0.101

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / Rfactor Rwork: 0.174 / Rfactor obs: 0.174
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 20 348 4552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Rfactor Rfree: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7

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