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- PDB-1dlg: CRYSTAL STRUCTURE OF THE C115S ENTEROBACTER CLOACAE MURA IN THE U... -

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Basic information

Entry
Database: PDB / ID: 1dlg
TitleCRYSTAL STRUCTURE OF THE C115S ENTEROBACTER CLOACAE MURA IN THE UN-LIGANDED STATE
ComponentsUDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
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
CYCLOHEXYLAMMONIUM ION / PHOSPHATE ION / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsSchonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N.
Citation
Journal: Biochemistry / Year: 2000
Title: Role of the loop containing residue 115 in the induced-fit mechanism of the bacterial cell wall biosynthetic enzyme MurA.
Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N.
#1: Journal: To be Published
Title: Comparative X-ray analysis of the un-liganded fosfomycin target MurA
Authors: Eschenburg, S. / Schonbrunn, E.
History
DepositionDec 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Nov 16, 2011Group: Atomic model
Revision 1.5Nov 3, 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 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,78214
Polymers89,6272
Non-polymers1,15512
Water18,3031016
1
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1985
Polymers44,8131
Non-polymers3854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5849
Polymers44,8131
Non-polymers7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,56428
Polymers179,2534
Non-polymers2,31124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area14440 Å2
ΔGint-117 kcal/mol
Surface area57440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.685, 155.532, 83.820
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1201-

HOH

21A-1205-

HOH

31A-1210-

HOH

41B-694-

HOH

51B-1200-

HOH

61B-1202-

HOH

71B-1203-

HOH

81B-1206-

HOH

Detailsthe asymmetric unit contains a homodimer (monomer A and monomer B)

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA


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


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.4-0.8 M sodium/potassium phosphate including 20-40 mM cyclohexylammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K, temperature 292K
Crystal grow
*PLUS
pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1325 mMsodium potassium phosphate1droppH6.9
21 mMdithiothreitol1drop
340 mg/mlprotein1drop
420 mMcyclohexylammonium phosphate1drop
51 Msodium potassium phospahte1reservoirpH6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8729
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.9→14.97 Å / Num. all: 703604 / Num. obs: 86085 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 35.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.119 / Num. unique all: 3179 / % possible all: 91.9
Reflection
*PLUS
Num. measured all: 703604
Reflection shell
*PLUS
% possible obs: 91.9 % / Mean I/σ(I) obs: 5.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→14.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2498822.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used 4 round of simulated annealing/minimization/bindividual refinement by CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2595 3 %random
Rwork0.173 ---
all0.173 86055 --
obs0.197 86055 98.9 %-
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20.69 Å2
2--1.99 Å20 Å2
3----4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 66 1016 7368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 435 3.1 %
Rwork0.205 13516 -
obs--96.4 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor Rfree: 0.246 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.205

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