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- PDB-7mfn: N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 7mfn
TitleN-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphylococcus aureus (strain MRSA USA300)
ComponentsN-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / Epimerase / NanE
Function / homology
Function and homology information


N-acylglucosamine-6-phosphate 2-epimerase / N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Putative N-acetylmannosamine-6-phosphate epimerase / Putative N-acetylmannosamine-6-phosphate epimerase / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
CITRIC ACID / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCurrie, M.J. / Dobson, R.C.J.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization.
Authors: Currie, M.J. / Manjunath, L. / Horne, C.R. / Rendle, P.M. / Subramanian, R. / Friemann, R. / Fairbanks, A.J. / Muscroft-Taylor, A.C. / North, R.A. / Dobson, R.C.J.
History
DepositionApr 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_radiation
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 / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BBB: N-acetylmannosamine-6-phosphate 2-epimerase
AAA: N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5437
Polymers49,0262
Non-polymers5175
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-49 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.999, 174.446, 44.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-acetylmannosamine-6-phosphate 2-epimerase / ManNAc-6-P epimerase


Mass: 24513.037 Da / Num. of mol.: 2 / Mutation: E180A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: nanE, BTN44_01590, EP54_02960, EQ90_08785, ERS072840_01491, FA040_00085, HMPREF3211_02501, NCTC10654_00351, NCTC10702_00560, NCTC7878_00328, RK64_02155
Production host: Escherichia coli (E. coli)
References: UniProt: X5EM89, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.55→46.4 Å / Num. obs: 87948 / % possible obs: 99.5 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 1.55→1.57 Å / Num. unique obs: 8254 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VVA

6vva


Resolution: 1.55→42.004 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.25 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1779 4414 5.019 %
Rwork0.1502 83534 -
all0.152 --
obs-87948 99.449 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.244 Å20 Å2-0 Å2
2--0.147 Å20 Å2
3---0.098 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 32 665 4131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133826
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173674
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.645234
X-RAY DIFFRACTIONr_angle_other_deg1.561.5798527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92523.687179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.5851518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024448
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02796
X-RAY DIFFRACTIONr_nbd_refined0.2440.2798
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23450
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2511
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.235
X-RAY DIFFRACTIONr_nbd_other0.2420.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2320.272
X-RAY DIFFRACTIONr_mcbond_it1.7161.7921937
X-RAY DIFFRACTIONr_mcbond_other1.6931.791936
X-RAY DIFFRACTIONr_mcangle_it2.3952.6892465
X-RAY DIFFRACTIONr_mcangle_other2.3982.692466
X-RAY DIFFRACTIONr_scbond_it2.8132.1391888
X-RAY DIFFRACTIONr_scbond_other2.8122.1411889
X-RAY DIFFRACTIONr_scangle_it4.3073.1032761
X-RAY DIFFRACTIONr_scangle_other4.3063.1042762
X-RAY DIFFRACTIONr_lrange_it6.16624.6274559
X-RAY DIFFRACTIONr_lrange_other6.16624.6264559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.548-1.5880.2632950.23757260.23864790.8830.88592.9310.215
1.588-1.6320.2353260.21259050.21362310.9110.9161000.19
1.632-1.6790.2223070.19358140.19561220.9290.93299.98370.169
1.679-1.730.2373110.1956400.19259510.920.9361000.165
1.73-1.7870.2162900.16955000.17157910.9390.94799.98270.147
1.787-1.850.1762870.15852830.15955700.9590.9581000.137
1.85-1.9190.23010.15750900.15953910.9490.9571000.138
1.919-1.9980.1822660.15749310.15951970.9550.9621000.142
1.998-2.0860.1782650.15147230.15249880.9610.9671000.139
2.086-2.1880.182250.14945450.1547700.9590.971000.139
2.188-2.3060.1812190.14343510.14445710.9590.97299.97810.136
2.306-2.4450.1682070.14441380.14543450.9640.9691000.139
2.445-2.6130.1541710.13539280.13640990.9720.9741000.134
2.613-2.8220.1671890.13835810.13937700.9670.9741000.141
2.822-3.090.1741680.14933520.1535200.9650.9691000.158
3.09-3.4520.1681560.1430640.14132200.970.9761000.154
3.452-3.9820.1431450.12626930.12728380.9780.9811000.146
3.982-4.8660.141220.12123360.12224580.9810.9841000.143
4.866-6.8350.1911030.16818240.16919270.9730.9761000.196
6.835-42.0040.221610.1811090.18211730.9650.96999.74420.227

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