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- PDB-7tb0: E. faecium MurAA in complex with fosfomycin and UNAG -

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Basic information

Entry
Database: PDB / ID: 7tb0
TitleE. faecium MurAA in complex with fosfomycin and UNAG
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / MurAA / Enterococcus faecium
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
[(1R)-1-hydroxypropyl]phosphonic acid / : / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: J.Biol.Chem. / Year: 2023
Title: Enolpyruvate transferase MurAA A149E , identified during adaptation of Enterococcus faecium to daptomycin, increases stability of MurAA-MurG interaction.
Authors: Zhou, Y. / Utama, B. / Pratap, S. / Supandy, A. / Song, X. / Tran, T.T. / Mehta, H.H. / Arias, C.A. / Shamoo, Y.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / Item: _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,05529
Polymers188,4634
Non-polymers3,59125
Water28,7521596
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,11710
Polymers47,1161
Non-polymers1,0019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9385
Polymers47,1161
Non-polymers8224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0007
Polymers47,1161
Non-polymers8846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0007
Polymers47,1161
Non-polymers8846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.030, 96.810, 96.821
Angle α, β, γ (deg.)115.06, 99.15, 103.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 1 - 420 / Label seq-ID: 1 - 420

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 47115.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: murA2_1, murA, A5804_000851, AWT83_08655, B4W81_09255, BU183_03490, CQR37_00415, CUM68_02040, CUN04_00930, CWC53_05360, DKP91_12610, DPX30_10805, DTPHA_1403386, EB12_00335, EB44_00320, F6440_ ...Gene: murA2_1, murA, A5804_000851, AWT83_08655, B4W81_09255, BU183_03490, CQR37_00415, CUM68_02040, CUN04_00930, CWC53_05360, DKP91_12610, DPX30_10805, DTPHA_1403386, EB12_00335, EB44_00320, F6440_10245, FIU59_00345, GBM73_14165
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A133CTP6, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Non-polymers , 6 types, 1621 molecules

#2: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FFQ / [(1R)-1-hydroxypropyl]phosphonic acid / Fosfomycin, bound form


Mass: 140.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O4P / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1596 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.26 % / Description: 3D needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.5mM UNAG and 2.5mM fosfomycin in the buffer containing 0.22 M Potassium sodium tartrate tetrahydrate, 26% w/v Polyethylene glycol 3,350, pH 7.4

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2018
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→46.99 Å / Num. obs: 257217 / % possible obs: 97.27 % / Redundancy: 4 % / Biso Wilson estimate: 16.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.1167 / Net I/σ(I): 9.09
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8275 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 25318 / CC1/2: 0.635 / Rrim(I) all: 0.956 / % possible all: 95.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R38

3r38


Resolution: 1.65→47.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.374 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15752 12707 4.9 %RANDOM
Rwork0.11593 ---
obs0.11788 244512 97.28 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0.09 Å20.1 Å2
2---0.02 Å2-0.79 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.65→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12721 0 205 1596 14522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01313252
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612846
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.63618022
X-RAY DIFFRACTIONr_angle_other_deg1.5131.57529452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14651714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1323.169669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.861152269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651580
X-RAY DIFFRACTIONr_chiral_restr0.1010.21851
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022842
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_it2.0181.6436787
X-RAY DIFFRACTIONr_mcbond_other2.0141.6436786
X-RAY DIFFRACTIONr_mcangle_it2.6362.4718500
X-RAY DIFFRACTIONr_mcangle_other2.6372.4718501
X-RAY DIFFRACTIONr_scbond_it2.892.0116465
X-RAY DIFFRACTIONr_scbond_other2.892.016466
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5462.8769515
X-RAY DIFFRACTIONr_long_range_B_refined4.41921.62114723
X-RAY DIFFRACTIONr_long_range_B_other4.0620.91714355
X-RAY DIFFRACTIONr_rigid_bond_restr3.77326098
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134440.07
12B134440.07
21A134380.06
22C134380.06
31A134140.07
32D134140.07
41B134060.06
42C134060.06
51B133870.06
52D133870.06
61C133460.06
62D133460.06
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 969 -
Rwork0.215 17717 -
obs--95.65 %

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