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- PDB-6q03: Crystal structure of MurA from Clostridium difficile in the prese... -

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Basic information

Entry
Database: PDB / ID: 6q03
TitleCrystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / clostridium difficile / peptidoglycan / antibiotics
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 speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDopkins, B.J. / Call, C.J. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: To Be Published
Title: Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)
Authors: Dopkins, B.J. / Call, C.J. / Thoden, J.B. / Holden, H.M.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)45,8683
Polymers45,1261
Non-polymers7412
Water6,666370
1
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)183,47012
Polymers180,5044
Non-polymers2,9668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area11020 Å2
ΔGint8 kcal/mol
Surface area52200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.946, 138.946, 138.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-968-

HOH

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Components

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


Mass: 45126.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: murA, CD630_01230 / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta(2)
References: UniProt: Q18CL1, 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.: 1 / Source method: obtained synthetically / Formula: C20H31N3O19P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000, 1M NMe4Cl, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→98.25 Å / Num. obs: 47927 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.087 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7205 / Rsym value: 0.46 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
PDB_EXTRACT3.25data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3swe

3swe


Resolution: 1.7→98.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.336 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2376 5 %RANDOM
Rwork0.1824 ---
obs0.1844 45551 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 21.802 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→98.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 48 370 3537
Biso mean--21.92 29.74 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193217
X-RAY DIFFRACTIONr_bond_other_d0.0010.023221
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9964357
X-RAY DIFFRACTIONr_angle_other_deg0.95837422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.47725.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 160 -
Rwork0.387 3226 -
all-3386 -
obs--93.74 %

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