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- PDB-5enz: S. aureus MnaA-UDP co-structure -

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Basic information

Entry
Database: PDB / ID: 5enz
TitleS. aureus MnaA-UDP co-structure
ComponentsUDP-GlcNAc 2-epimerase
KeywordsISOMERASE / SUGAR-NUCLEOTIDE EPIMERASE / ROSSMANN FOLD / TWO DOMAINS / GLYCOGEN PHOSPHORYLASE SUPERFAMILY / UDP / DIMER
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsFischmann, T.O.
CitationJournal: Plos Pathog. / Year: 2016
Title: Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets.
Authors: Mann, P.A. / Muller, A. / Wolff, K.A. / Fischmann, T. / Wang, H. / Reed, P. / Hou, Y. / Li, W. / Muller, C.E. / Xiao, J. / Murgolo, N. / Sher, X. / Mayhood, T. / Sheth, P.R. / Mirza, A. / ...Authors: Mann, P.A. / Muller, A. / Wolff, K.A. / Fischmann, T. / Wang, H. / Reed, P. / Hou, Y. / Li, W. / Muller, C.E. / Xiao, J. / Murgolo, N. / Sher, X. / Mayhood, T. / Sheth, P.R. / Mirza, A. / Labroli, M. / Xiao, L. / McCoy, M. / Gill, C.J. / Pinho, M.G. / Schneider, T. / Roemer, T.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-GlcNAc 2-epimerase
B: UDP-GlcNAc 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,00911
Polymers87,3782
Non-polymers1,6319
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-19 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 82.780, 170.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-GlcNAc 2-epimerase / UDP-N-acetylglucosamine 2-epimerase


Mass: 43688.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: mnaA, mnaA_2, AL078_07320, AM595_10995, EQ80_010635, ER12_010620, ERS365775_02407, ERS410449_02295, ERS411009_02507, ERS411017_02562, ERS445051_02067, ERS445052_01290, RL02_00620, RT87_10865, SAFDA_1985, TM61_09075
Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9REV4, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% v/v PEG 400 0.1M Li2SO4, 0.1M NaCacodylate pH 6.5, 4mM Na2UDP
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→170.88 Å / Num. obs: 60512 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Net I/σ(I): 25.1 / Num. measured all: 370100
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.91-2.146.20.3694.8104877169620.9520.161100
4.27-170.885.80.02167.933064573110.00999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimless0.1.27data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
PHENIXmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6D

1f6d


Resolution: 1.91→74.5 Å / Cor.coef. Fo:Fc: 0.9397 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3062 5.07 %RANDOM
Rwork0.2037 ---
obs0.2049 60432 99.76 %-
Displacement parametersBiso mean: 41.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.8066 Å20 Å20 Å2
2---10.0876 Å20 Å2
3---6.281 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 1.91→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5843 0 99 187 6129
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111964HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0421660HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1699HARMONIC5
X-RAY DIFFRACTIONt_it11964HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion16.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion798SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12942SEMIHARMONIC4
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2316 226 5.26 %
Rwork0.2097 4067 -
all0.2109 4293 -
obs--97.68 %

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