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- PDB-3swg: AQUIFEX AEOLICUS MurA in complex with UDP-N-acetylmuramic acid an... -

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Basic information

Entry
Database: PDB / ID: 3swg
TitleAQUIFEX AEOLICUS MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys124
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 / 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
Chem-EPZ / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
CitationJournal: To be Published
Title: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5
Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...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 / 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 0THIS ENTRY 3SWG REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2YVWSF DETERMINED ...THIS ENTRY 3SWG REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2YVWSF DETERMINED BY AUTHORS OF THE PDB ENTRY 2YVW: AUTHOR Y.KITAMURA,S.YOKOYAMA,S.KURAMITSU
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 2YVW.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,79819
Polymers47,4911
Non-polymers2,30718
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.000, 132.000, 58.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-924-

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: 47490.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: murA, aq_1281 / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O67315, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Non-polymers , 6 types, 366 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N3O19P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Version: 1.3 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YVW

2yvw


Resolution: 1.81→43.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 91849.69 / 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
Rfree0.19 2516 5 %RANDOM
Rwork0.165 ---
obs0.165 50320 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.7235 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.26 Å20 Å20 Å2
2---9.26 Å20 Å2
3---18.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.81→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 151 348 3769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 1.81→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 351 5.2 %
Rwork0.236 6344 -
obs--75.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cpa.parcpa.top
X-RAY DIFFRACTION3epu.parepu.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5pg4.parpg4.top
X-RAY DIFFRACTION6pge.parpge.top
X-RAY DIFFRACTION7peg.parpeg.top
X-RAY DIFFRACTION8edo.paredo.top

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