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- PDB-3swd: E. coli MurA in complex with UDP-N-acetylmuramic acid and covalen... -

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Basic information

Entry
Database: PDB / ID: 3swd
TitleE. coli MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys115
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 / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
CitationJournal: Biochemistry / Year: 2009
Title: Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .
Authors: Jackson, S.G. / Zhang, F. / Chindemi, P. / Junop, M.S. / Berti, P.J.
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: 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_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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 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 3SWD REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3ISSSF DETERMINED ...THIS ENTRY 3SWD REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3ISSSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3ISS: AUTHOR S.G.JACKSON,F.ZHANG,P.CHINDEMI,M.S.JUNOP,P.J.BERTI
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 3ISS.

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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
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
I: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
J: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
K: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
L: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,09024
Polymers538,93712
Non-polymers8,15312
Water14,250791
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers44,9111
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,3638
Polymers179,6464
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-30 kcal/mol
Surface area52480 Å2
MethodPISA
14
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,3638
Polymers179,6464
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-30 kcal/mol
Surface area52700 Å2
MethodPISA
15
I: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
J: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
K: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
L: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,3638
Polymers179,6464
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-29 kcal/mol
Surface area53230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.510, 120.910, 139.730
Angle α, β, γ (deg.)111.52, 104.44, 90.19
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 44911.449 Da / Num. of mol.: 12 / Mutation: N67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3189, JW3156, murA, murZ / Plasmid: PET41A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A749, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: 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.: 12 / Source method: obtained synthetically / Formula: C20H31N3O19P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.37 Å3/Da / Density % sol: 48.18 %

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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 3ISS

3iss


Resolution: 2.5→47.48 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2837044.55 / 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
Rfree0.28 8367 5 %RANDOM
Rwork0.226 ---
obs0.226 167316 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4465 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 57.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å21.29 Å24.09 Å2
2---4.04 Å2-1.92 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37716 0 528 791 39035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d11.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.21.5
X-RAY DIFFRACTIONc_mcangle_it10.072
X-RAY DIFFRACTIONc_scbond_it11.792
X-RAY DIFFRACTIONc_scangle_it13.552.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 1368 4.9 %
Rwork0.318 26414 -
obs--97.3 %

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