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- PDB-1naw: ENOLPYRUVYL TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1naw
TitleENOLPYRUVYL TRANSFERASE
ComponentsUDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
KeywordsTRANSFERASE / PEPTIDOGLYCAN BIOSYNTHESIS / HINGE / DOMAIN MOVEMENT / SEQUENCE MOTIF / FOLDING
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 / cytoplasm
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
CYCLOHEXYLAMMONIUM ION / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsSchoenbrunn, E. / Sack, S. / Eschenburg, S. / Perrakis, A. / Krekel, F. / Amrhein, N. / Mandelkow, E.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin.
Authors: Schonbrunn, E. / Sack, S. / Eschenburg, S. / Perrakis, A. / Krekel, F. / Amrhein, N. / Mandelkow, E.
#1: Journal: J.Struct.Biol. / Year: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Udp-N-Acetylglucosamine Enolpyruvyltransferase of Enterobacter Cloacae
Authors: Sack, S. / Dauter, Z. / Wanke, C. / Amrhein, N. / Mandelkow, E. / Schonbrunn, E.
#2: Journal: FEBS Lett. / Year: 1992
Title: The Udp-N-Acetylglucosamine 1-Carboxyvinyl-Transferase of Enterobacter Cloacae. Molecular Cloning, Sequencing of the Gene and Overexpression of the Enzyme
Authors: Wanke, C. / Falchetto, R. / Amrhein, N.
History
DepositionJul 23, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
B: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8574
Polymers89,6572
Non-polymers2002
Water8,611478
1
A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
B: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
B: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7148
Polymers179,3144
Non-polymers4014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
2
A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE

B: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)179,7148
Polymers179,3144
Non-polymers4014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area10700 Å2
ΔGint-39 kcal/mol
Surface area54990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.900, 155.900, 83.850
Angle α, β, γ (deg.)90.00, 91.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21B-488-

HOH

31B-540-

HOH

41B-599-

HOH

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYL-TRANSFERASE


Mass: 44828.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 105 (PHARMACIA LKB)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENOLPYRUVYL TRANSFERASE IS A KEY ENZYME IN PEPTIDOGLYCAN BIOSYNTHESIS.

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD USING PLASTIC TISSUE CULTURE PLATES. 0.4 M SODIUM/POTASSIUM PHOSPHATE BUFFER (PH 6.4) CONTAINING 40 MM CYCLOHEXYLAMMONIUM ...Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD USING PLASTIC TISSUE CULTURE PLATES. 0.4 M SODIUM/POTASSIUM PHOSPHATE BUFFER (PH 6.4) CONTAINING 40 MM CYCLOHEXYLAMMONIUM PHOSPHATE WERE EQUILIBRATED AGAINST 1 ML 0.8 M SODIUM/POTASSIUM PHOSPHATE BUFFER (PH 6.4). CRYSTALLIZATION USUALLY OCCURRED WITHIN 3 DAYS AND THE CRYSTALS REACHED THEIR MAXIMUM SIZE OF 0.5 X 0.5 X 0.1 MM==3== AFTER 5 DAYS AT ROOM TEMPERATURE. (SEE REFERENCE 1 FOR DETAILS.), vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8 Msodium/potassium phosphate1drop
240 mMctclohexylammonium phosphate1drop
30.8 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1995
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 103189 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.29 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 744941
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameClassification
PHASESphasing
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→10 Å
RfactorNum. reflection% reflection
Rfree0.27 14800 10 %
Rwork0.197 --
obs-147378 99.9 %
Displacement parametersBiso mean: 23.1 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 14 478 6776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1654
X-RAY DIFFRACTIONp_mcangle_it4.1485
X-RAY DIFFRACTIONp_scbond_it6.2636
X-RAY DIFFRACTIONp_scangle_it8.588
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1980.3
X-RAY DIFFRACTIONp_planar_tor2.3933
X-RAY DIFFRACTIONp_staggered_tor18.4415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.0620
X-RAY DIFFRACTIONp_special_tor

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