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- PDB-1q3g: MurA (Asp305Ala) liganded with tetrahedral reaction intermediate -

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Basic information

Entry
Database: PDB / ID: 1q3g
TitleMurA (Asp305Ala) liganded with tetrahedral reaction intermediate
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / inside-out alpha-beta barrel
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
Chem-UDA / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsEschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral ...Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral Reaction Intermediate States.
Authors: Eschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
History
DepositionJul 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: 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 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
W: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
X: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Y: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Z: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)729,96648
Polymers716,56616
Non-polymers13,39932
Water25,7791431
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)182,49112
Polymers179,1424
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)182,49112
Polymers179,1424
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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)182,49112
Polymers179,1424
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
W: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
X: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Y: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Z: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,49112
Polymers179,1424
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.459, 153.934, 167.481
Angle α, β, γ (deg.)90.00, 112.95, 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: 44785.398 Da / Num. of mol.: 16 / Mutation: N67D,D305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: MURA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-UDA / 3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 775.396 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C20H32N3O23P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1431 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein1drop
210 mMMES1reservoirpH6.4
310 %(w/v)PEG200001reservoir
45 mMUNAG1reservoir
55 mMPEP1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 185835 / Num. obs: 185835 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9008 / % possible all: 95.9
Reflection
*PLUS
Num. obs: 809759 / % possible obs: 98.9 %
Reflection shell
*PLUS
Lowest resolution: 2.7 Å / % possible obs: 0.335 % / Num. unique obs: 26280 / Num. measured obs: 95.9

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A2N

1a2n


Resolution: 2.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 3716 random
Rwork0.217 --
obs0.217 185835 -
all-185835 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.115 Å20 Å2-5.37 Å2
2---0.264 Å20 Å2
3----7.85 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50240 0 848 1431 52519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.24747
X-RAY DIFFRACTIONc_mcbond_it2.0571.5
X-RAY DIFFRACTIONc_mcangle_it3.1472
X-RAY DIFFRACTIONc_scbond_it3.5272
X-RAY DIFFRACTIONc_scangle_it5.0572.5
LS refinement shellResolution: 2.65→2.67 Å
RfactorNum. reflection
Rfree0.428 62
Rwork0.353 -
obs-3050
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3unt_etg.par
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cis_peptide.param
Refinement
*PLUS
% reflection Rfree: 2 % / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.25
LS refinement shell
*PLUS
Lowest resolution: 2.7 Å

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