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- PDB-1eyn: Structure of mura liganded with the extrinsic fluorescence probe ANS -

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Basic information

Entry
Database: PDB / ID: 1eyn
TitleStructure of mura liganded with the extrinsic fluorescence probe ANS
ComponentsUDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
KeywordsTRANSFERASE / inside-out alpha-beta barrel / L-isoaspartate in position 67
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / 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
8-ANILINO-1-NAPHTHALENE SULFONATE / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSchonbrunn, E. / Eschenburg, S. / Luger, K. / Kabsch, W. / Amrhein, N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structural basis for the interaction of the fluorescence probe 8-anilino-1-naphthalene sulfonate (ANS) with the antibiotic target MurA.
Authors: Schonbrunn, E. / Eschenburg, S. / Luger, K. / Kabsch, W. / Amrhein, N.
#1: Journal: Proteins / Year: 2000
Title: Comparative X-ray Analysis of the Un-liganded Fosfomycin-Target MurA
Authors: Eschenburg, S. / Schonbrunn, E.
#2: Journal: Biochemistry / Year: 2000
Title: Role of the Loop Containing Residue 115 in the Induced-fit Mechanism of the Bacterial Cell Wall Biosynthetic Enzyme MurA
Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N.
History
DepositionMay 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3134
Polymers44,8291
Non-polymers4843
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.100, 66.600, 107.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE / / ENOYLPYRUVATE TRANSFERASE / EPT / MURA


Mass: 44829.406 Da / Num. of mol.: 1 / Mutation: N67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE / 8-Anilinonaphthalene-1-sulfonic acid


Mass: 299.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13NO3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES/PEG20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMMes/NaOH11
25 %PEG2000011
32.5 mMANS11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→29.33 Å / Num. all: 1222364 / Num. obs: 49890 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 10 % / Rmerge(I) obs: 0.29 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 1222364
Reflection shell
*PLUS
% possible obs: 98.3 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 1EJC

1ejc


Resolution: 1.7→29.33 Å / Isotropic thermal model: Restrained / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1541 -random
Rwork0.18 ---
all-49890 --
obs-49568 99.2 %-
Solvent computationSolvent model: Flat Model / Bsol: 85.013 Å2 / ksol: 0.4529 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å20 Å20 Å2
2---1.47 Å20 Å2
3---5.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 33 506 3682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d2.28
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 243 3 %
Rwork0.348 7750 -
obs--97.4 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.28

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