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- PDB-3swq: E. Cloacae MurA in complex with Enolpyruvyl-UNAG -

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Basic information

Entry
Database: PDB / ID: 3swq
TitleE. Cloacae MurA in complex with Enolpyruvyl-UNAG
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / MURA / CLOSE ENZYME STATE / CELL WALL / BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS
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
ACETATE ION / Chem-EPU / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsZhu, J.-Y. / Yang, Y. / Schonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA).
Authors: Zhu, J.Y. / Yang, Y. / Han, H. / Betzi, S. / Olesen, S.H. / Marsilio, F. / Schonbrunn, E.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Sep 13, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)46,87722
Polymers44,8291
Non-polymers2,04821
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.300, 138.300, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

21A-679-

HOH

31A-759-

HOH

41A-782-

HOH

51A-807-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 44829.406 Da / Num. of mol.: 1 / Mutation: N67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: murA, murZ, ECL_04571 / Plasmid: PET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Non-polymers , 6 types, 436 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N3O19P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsIAS67 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 20 mg/mL MurA, 5 mM UNAG, 25 mM HEPES, 100 mM Ammonium Acetate, 50 mM Bis-Tris, 12.5% PEG 3,350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 13, 2010 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 38692 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 15.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.075 / Net I/σ(I): 25
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
XDSdata scaling
CNS1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SU9

3su9


Resolution: 1.83→19.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6499442.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1121 2.9 %RANDOM
Rwork0.16 ---
obs0.16 38692 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6804 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.83→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 133 415 3691
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d12.52
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.472.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 186 2.9 %
Rwork0.187 6243 -
obs--99.9 %

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