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- PDB-1a2n: STRUCTURE OF THE C115A MUTANT OF MURA COMPLEXED WITH THE FLUORINA... -

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Basic information

Entry
Database: PDB / ID: 1a2n
TitleSTRUCTURE OF THE C115A MUTANT OF MURA COMPLEXED WITH THE FLUORINATED ANALOG OF THE REACTION TETRAHEDRAL INTERMEDIATE
ComponentsUDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
KeywordsTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / ENOLPYRUVYL TRANSFERASE / UDP-N-ACETYLGLUCOSAMINE
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / : / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
Chem-TET / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT / Resolution: 2.8 Å
AuthorsSkarzynski, T.
Citation
Journal: Biochemistry / Year: 1998
Title: Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral ...Title: Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral intermediate bound to the active site of the C115A mutant of MurA
Authors: Skarzynski, T. / Kim, D.H. / Lees, W.J. / Walsh, C.T. / Duncan, K.
#1: Journal: Structure / Year: 1996
Title: Structure of Udp-N-Acetylglucosamine Enolpyruvyl Transferase, an Enzyme Essential for the Synthesis of Bacterial Peptidoglycan, Complexed with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin
Authors: Skarzynski, T. / Mistry, A. / Wonacott, A. / Hutchinson, S.E. / Kelly, V.A. / Duncan, K.
History
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 14, 2019Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6332
Polymers44,8391
Non-polymers7931
Water4,882271
1
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8996
Polymers134,5183
Non-polymers2,3803
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
Unit cell
Length a, b, c (Å)111.150, 111.150, 67.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE / MURA


Mass: 44839.477 Da / Num. of mol.: 1 / Mutation: C115A
Source method: isolated from a genetically manipulated source
Details: LIGAND IS THE FLUORINATED ANALOG OF THE REACTION TETRAHEDRAL INTERMEDIATE
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A749, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-TET / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL-3-FLUORO-2-PHOSPHONOOXY)PROPIONIC ACID


Mass: 793.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31FN3O23P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.68 Å3/Da / Density % sol: 55 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 40% TERT-BUTANOL, 100 MM CACL2, 100 MM TRIS-HCL, PH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
225 %tert-butyl alcohol1reservoir
3100 mM1reservoirCaCl2
4100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 5, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→19.5 Å / Num. obs: 11692 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
PROLSQrefinement
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB ENTRY 1UAE

1uae


Resolution: 2.8→10 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 11741 99.2 %
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 50 422 3600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.235 1465 -
obs--100 %

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