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- PDB-3lth: E. cloacae MurA dead-end complex with UNAG and fosfomycin -

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Basic information

Entry
Database: PDB / ID: 3lth
TitleE. cloacae MurA dead-end complex with UNAG and fosfomycin
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / open enzyme state / inside-out alpha/beta barrel / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Transferase / TRANSFERASE-ANTIBIOTIC complex
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
[(1R)-1-hydroxypropyl]phosphonic acid / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchonbrunn, E.
CitationJournal: Biochemistry / Year: 2010
Title: The fungal product terreic acid is a covalent inhibitor of the bacterial cell wall biosynthetic enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) .
Authors: Han, H. / Yang, Y. / Olesen, S.H. / Becker, A. / Betzi, S. / Schonbrunn, E.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5773
Polymers44,8291
Non-polymers7472
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 64.200, 116.200
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 / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 44829.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: murA, murZ / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-FFQ / [(1R)-1-hydroxypropyl]phosphonic acid / Fosfomycin, bound form / Fosfomycin


Mass: 140.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O4P / Comment: antibiotic*YM
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE UNBOUND FORM OF THE ANTIBIOTIC IS FOSFOMYCIN. UPON REACTION WITH PROTEIN, IT COVALENTLY BINDS ...THE UNBOUND FORM OF THE ANTIBIOTIC IS FOSFOMYCIN. UPON REACTION WITH PROTEIN, IT COVALENTLY BINDS TO CYS115. FFQ REPRESENTS THE BOUND FORM OF FOSFOMYCIN.
Sequence detailsASP67 FORMS AN ISOPEPTIDIC BOND AND IS A RESULT OF POSTTRANSLATIONAL MODIFICATION OF ASN67

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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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12.5 mM MES/NaOH (pH 6.2), 25 mM Na/K phosphate buffer, 6% (w/v) polyethylene glycol 20000, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 4, 1999 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 46694 / Num. obs: 46694 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.7
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3050 / % possible all: 98.9

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAE

1uae


Resolution: 1.75→19.92 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1450 -random
Rwork0.172 ---
all0.172 46638 --
obs0.172 46638 98.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 47 523 3713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.339 213 -
Rwork0.313 --
obs-7174 95.2 %

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