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- PDB-3swe: Haemophilus influenzae MurA in complex with UDP-N-acetylmuramic a... -

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Basic information

Entry
Database: PDB / ID: 3swe
TitleHaemophilus influenzae MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys117
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 / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin.
Authors: Yoon, H.J. / Lee, S.J. / Mikami, B. / Park, H.J. / Yoo, J. / Suh, S.W.
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 3SWE REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2RL1SF DETERMINED ...THIS ENTRY 3SWE REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2RL1SF DETERMINED BY AUTHORS OF THE PDB ENTRY 2RL1: AUTHOR H.J.YOON,S.W.SUH
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 2RL1.

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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)46,7499
Polymers45,4051
Non-polymers1,3448
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)186,99536
Polymers181,6194
Non-polymers5,37632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14460 Å2
ΔGint-255 kcal/mol
Surface area52570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.910, 123.380, 127.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

21A-890-

HOH

31A-912-

HOH

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Components

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


Mass: 45404.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1081, murA, murZ / Plasmid: PET-21A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P45025, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.77 Å3/Da / Density % sol: 55.6 %

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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 2RL1

2rl1


Resolution: 2.2→28.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 147996.35 / 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
Rfree0.238 2594 10.2 %RANDOM
Rwork0.186 ---
obs0.186 25353 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0664 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-20.93 Å20 Å20 Å2
2---8.7 Å20 Å2
3----12.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 81 318 3547
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 427 10.5 %
Rwork0.238 3633 -
obs--95.1 %

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