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- PDB-7mfs: N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus a... -

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Basic information

Entry
Database: PDB / ID: 7mfs
TitleN-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with substrate and product bound
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
N-acetylmannosamine-6-phosphate / N-acetyl-D-glucosamine-6-phosphate / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Structure summary / Category: citation / citation_author / entity
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 / _entity.pdbx_description
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)50,48510
Polymers49,1422
Non-polymers1,3438
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-82 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.928, 76.474, 174.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 24571.072 Da / Num. of mol.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LRY / N-acetylmannosamine-6-phosphate


Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-RFW / N-acetyl-D-glucosamine-6-phosphate


Mass: 299.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14NO9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
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: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.51→46.25 Å / Num. obs: 91961 / % possible obs: 98.73 % / Redundancy: 30.1 % / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 1.51→1.56 Å / Num. unique obs: 8946 / CC1/2: 0.661

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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: 1.51→46.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.506 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2099 4620 5.024 %
Rwork0.1798 87341 -
all0.181 --
obs-91961 98.725 %
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: 12.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.624 Å20 Å20 Å2
2---0.207 Å20 Å2
3----0.417 Å2
Refinement stepCycle: LAST / Resolution: 1.51→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 80 596 4116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133904
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173767
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6425357
X-RAY DIFFRACTIONr_angle_other_deg1.4771.5818759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11223.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44815711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.1251519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024478
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02816
X-RAY DIFFRACTIONr_nbd_refined0.240.2856
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23608
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21852
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2501
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.238
X-RAY DIFFRACTIONr_nbd_other0.2120.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.264
X-RAY DIFFRACTIONr_mcbond_it1.2061.0651925
X-RAY DIFFRACTIONr_mcbond_other1.1991.0621924
X-RAY DIFFRACTIONr_mcangle_it1.9151.5932447
X-RAY DIFFRACTIONr_mcangle_other1.9161.5962448
X-RAY DIFFRACTIONr_scbond_it1.851.3591978
X-RAY DIFFRACTIONr_scbond_other1.8491.3611979
X-RAY DIFFRACTIONr_scangle_it2.8771.9592886
X-RAY DIFFRACTIONr_scangle_other2.8761.9612887
X-RAY DIFFRACTIONr_lrange_it6.18515.5664633
X-RAY DIFFRACTIONr_lrange_other6.13115.3914596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5490.3423290.316300X-RAY DIFFRACTION97.428
1.549-1.5920.3122980.2626136X-RAY DIFFRACTION97.4111
1.592-1.6380.253330.2326008X-RAY DIFFRACTION97.9003
1.638-1.6880.2373250.2075809X-RAY DIFFRACTION97.8153
1.688-1.7440.2222940.1965662X-RAY DIFFRACTION98.0896
1.744-1.8050.242830.1985512X-RAY DIFFRACTION98.6887
1.805-1.8730.2233020.1955301X-RAY DIFFRACTION98.3673
1.873-1.9490.2152970.1955120X-RAY DIFFRACTION98.8865
1.949-2.0360.2232530.1914960X-RAY DIFFRACTION98.8996
2.036-2.1350.2042490.1874738X-RAY DIFFRACTION98.968
2.135-2.2510.2092340.1794555X-RAY DIFFRACTION99.2333
2.251-2.3870.1792090.1634327X-RAY DIFFRACTION99.4737
2.387-2.5520.2072130.174046X-RAY DIFFRACTION99.4861
2.552-2.7560.1832080.163819X-RAY DIFFRACTION99.6782
2.756-3.0190.2221650.1673499X-RAY DIFFRACTION99.8093
3.019-3.3740.1911670.1643230X-RAY DIFFRACTION99.8824
3.374-3.8960.181460.152831X-RAY DIFFRACTION99.9329
3.896-4.7690.1541420.1252436X-RAY DIFFRACTION100
4.769-6.7340.1861090.1541914X-RAY DIFFRACTION100
6.734-46.250.232640.1761138X-RAY DIFFRACTION99.751

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