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- PDB-1ryw: C115S MurA liganded with reaction products -

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Basic information

Entry
Database: PDB / ID: 1ryw
TitleC115S MurA liganded with reaction products
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / inside-out alpha-beta barrel
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-EPU / PHOSPHATE ION / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEschenburg, S. / Schonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Evidence That the Fosfomycin Target Cys115 in UDP-N-acetylglucosamine Enolpyruvyl Transferase (MurA) Is Essential for Product Release.
Authors: Eschenburg, S. / Priestman, M. / Schonbrunn, E.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN HET GROUPS NUMBERED 2000+ ARE ASSOCIATED WITH CHAIN A. HET GROUPS NUMBERED 3000+ ARE ...HETEROGEN HET GROUPS NUMBERED 2000+ ARE ASSOCIATED WITH CHAIN A. HET GROUPS NUMBERED 3000+ ARE ASSOCIATED WITH CHAIN B. HET GROUPS NUMBERED 4000+ ARE ASSOCIATED WITH CHAIN C. HET GROUPS NUMBERED 5000+ ARE ASSOCIATED WITH CHAIN D. HET GROUPS NUMBERED 6000+ ARE ASSOCIATED WITH CHAIN E. HET GROUPS NUMBERED 7000+ ARE ASSOCIATED WITH CHAIN F. HET GROUPS NUMBERED 8000+ ARE ASSOCIATED WITH CHAIN G. HET GROUPS NUMBERED 9000+ ARE ASSOCIATED WITH CHAIN H.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,34642
Polymers358,5078
Non-polymers7,84034
Water32,7151816
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,35623
Polymers179,2534
Non-polymers4,10319
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17670 Å2
ΔGint-81 kcal/mol
Surface area51020 Å2
MethodPISA
2
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,99019
Polymers179,2534
Non-polymers3,73715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-86 kcal/mol
Surface area51040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.867, 153.729, 135.089
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44813.344 Da / Num. of mol.: 8 / Mutation: N67D,C115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: MURA, MURZ / Production host: Escherichia coli (E. coli)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H29N3O19P2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1816 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 140111 / Num. obs: 140111 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Num. unique all: 6835 / Rsym value: 0.35 / % possible all: 97.3

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Processing

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

1ejc


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2627 -random
Rwork0.178 ---
all0.178 131328 --
obs0.178 131328 99 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25144 0 499 1816 27459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.3→2.34 Å
RfactorNum. reflection% reflection
Rfree0.225 2627 -
Rwork0.178 --
obs-6835 99 %

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