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- PDB-8d84: E. faecium MurAA in complex with UDP-N-acetylmuramic acid (UNAM) ... -

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Basic information

Entry
Database: PDB / ID: 8d84
TitleE. faecium MurAA in complex with UDP-N-acetylmuramic acid (UNAM) and a covalent adduct of PEP with Cys119
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / MurAA
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 / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
Chem-EPZ / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhou, Y. / Shamoo, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 A1080714 United States
CitationJournal: To Be Published
Title: E. faecium MurAA in complex with fosfomycin and UNAG
Authors: Zhou, Y. / Shamoo, Y.
History
DepositionJun 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

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)575,56024
Polymers567,40712
Non-polymers8,15312
Water88349
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,8538
Polymers189,1364
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-20 kcal/mol
Surface area51810 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules

F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,8538
Polymers189,1364
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area9870 Å2
ΔGint-17 kcal/mol
Surface area52190 Å2
MethodPISA
3
I: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
K: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules

J: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules

L: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,8538
Polymers189,1364
Non-polymers2,7184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_345-x-2,y-1/2,-z+1/21
Buried area9900 Å2
ΔGint-21 kcal/mol
Surface area52020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.865, 168.376, 316.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11E-602-

HOH

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Components

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


Mass: 47283.887 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: murA, EGW70_02335 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A3N3SEJ7, 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: isolated from a natural source / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.1 M DL-Malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.65→49.81 Å / Num. obs: 225455 / % possible obs: 99.78 % / Redundancy: 15.1 % / Biso Wilson estimate: 63.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2363 / Net I/σ(I): 11.32
Reflection shellResolution: 2.65→2.749 Å / Rmerge(I) obs: 3.063 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 22047 / CC1/2: 0.368

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r38

3r38


Resolution: 2.65→49.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.907 / SU B: 33.332 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26067 11318 5 %RANDOM
Rwork0.24094 ---
obs0.24195 214123 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.416 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å2-0 Å20 Å2
2--0.48 Å2-0 Å2
3----2.49 Å2
Refinement stepCycle: 1 / Resolution: 2.65→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38209 0 528 49 38786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01239434
X-RAY DIFFRACTIONr_bond_other_d0.0010.01636729
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.63753600
X-RAY DIFFRACTIONr_angle_other_deg2.281.54785385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16355052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.159.538260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85106714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.26382
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0244896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026896
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8543.52620172
X-RAY DIFFRACTIONr_mcbond_other2.8543.52620172
X-RAY DIFFRACTIONr_mcangle_it4.3525.29125200
X-RAY DIFFRACTIONr_mcangle_other4.3525.29125201
X-RAY DIFFRACTIONr_scbond_it5.0544.27519262
X-RAY DIFFRACTIONr_scbond_other5.0544.27619263
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9826.31228389
X-RAY DIFFRACTIONr_long_range_B_refined11.42848.20339797
X-RAY DIFFRACTIONr_long_range_B_other11.42848.20539798
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.654→2.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 811 -
Rwork0.343 15379 -
obs--97.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.848-0.18370.3470.8167-0.27040.9358-0.03280.0211-0.0423-0.01560.0594-0.20890.00150.0492-0.02660.08580.0115-0.06110.3633-0.06370.4153-65.164-57.518331.004
21.00550.16520.08261.31710.14270.90910.01910.01860.04260.1894-0.01290.2319-0.0359-0.1759-0.00620.09390.04370.00630.40750.01750.3705-99.6427-56.671242.8796
30.8924-0.08660.08781.27090.47091.1545-0.108-0.02020.0413-0.15970.03760.2453-0.2803-0.11930.07040.1930.0564-0.08540.28530.01890.3121-79.8105-12.741131.5279
40.74590.2693-0.2350.8440.23081.2155-0.07040.0623-0.26820.1070.03820.00860.1475-0.06590.03220.14990.01-0.03080.28660.01350.3731-97.139-93.009550.1944
50.4977-0.0724-0.07490.784-0.29591.4857-0.06730.0263-0.20950.02490.0228-0.16850.21180.1540.04450.10210.0362-0.04270.3448-0.07370.5027-67.3216-94.609629.3005
60.74360.16130.28060.96330.23892.1231-0.23060.01340.22820.09510.09270.0767-0.891-0.36970.13790.63560.1991-0.11640.16680.03790.183-98.3338-62.4717104.2916
70.97720.0087-0.01541.2147-0.34181.7233-0.2304-0.06960.28080.37150.0305-0.2589-0.94990.23880.20.787-0.1623-0.25960.0952-0.03720.2243-69.491-59.9206126.5928
80.90060.04260.2421.1405-0.03451.5011-0.03720.1534-0.04430.05190.1254-0.1278-0.19080.3215-0.08820.1557-0.0421-0.05750.3553-0.08860.268-45.9127-14.330345.038
91.6354-0.57690.73351.0605-0.70941.45070.11440.0849-0.007-0.072-0.1662-0.12480.19870.18820.05180.09950.0738-0.06340.36550.05520.3524-131.7388-91.445173.3715
101.7659-0.21540.8581.290.14761.23510.0058-0.22870.14650.0261-0.07240.2062-0.0385-0.24130.06660.06440.0538-0.09210.4097-0.0440.4668-28.9166-65.63866.3504
111.2466-0.24170.39491.2048-0.03891.24590.00770.13680.44040.0133-0.0621-0.2449-0.03510.10320.05440.05330.0243-0.09480.34790.0630.6129-140.6538-55.961868.375
121.60760.61810.18581.6746-0.11121.22440.10860.4388-0.4937-0.00350.0572-0.48590.03890.2163-0.16580.06150.018-0.09670.4696-0.19210.5918-127.0775-14.291277.0138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 420
2X-RAY DIFFRACTION2B1 - 420
3X-RAY DIFFRACTION3C1 - 420
4X-RAY DIFFRACTION4D1 - 420
5X-RAY DIFFRACTION5E1 - 420
6X-RAY DIFFRACTION6F1 - 420
7X-RAY DIFFRACTION7G1 - 420
8X-RAY DIFFRACTION8H1 - 420
9X-RAY DIFFRACTION9I1 - 420
10X-RAY DIFFRACTION10J1 - 420
11X-RAY DIFFRACTION11K1 - 420
12X-RAY DIFFRACTION12L1 - 420

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