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

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Basic information

Entry
Database: PDB / ID: 7mqt
TitleN-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with 5-deoxy substrate 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
CITRIC ACID / Chem-ZM1 / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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
DepositionMay 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1688
Polymers49,1422
Non-polymers1,0266
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-57 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.437, 173.454, 44.040
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: 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-ZM1 / 2-acetamido-2,5-dideoxy-6-O-phosphono-D-lyxo-hexose


Mass: 285.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.88→46.11 Å / Num. obs: 48503 / % possible obs: 99.67 % / Redundancy: 7.2 % / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 4640 / CC1/2: 0.702

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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: 1.88→46.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.035 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1967 2470 5.092 %
Rwork0.1539 46033 -
all0.156 --
obs-48503 99.659 %
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: 21.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.164 Å20 Å20 Å2
2---0.539 Å20 Å2
3---0.375 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 64 581 4087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173619
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6525165
X-RAY DIFFRACTIONr_angle_other_deg1.4551.5888395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37523.825183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7615678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.511518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024336
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02784
X-RAY DIFFRACTIONr_nbd_refined0.2160.2853
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23744
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21886
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2524
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.221
X-RAY DIFFRACTIONr_nbd_other0.1890.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2260.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_mcbond_it1.6471.9681874
X-RAY DIFFRACTIONr_mcbond_other1.6391.9651873
X-RAY DIFFRACTIONr_mcangle_it2.3562.9412370
X-RAY DIFFRACTIONr_mcangle_other2.3632.9432371
X-RAY DIFFRACTIONr_scbond_it2.7082.3421901
X-RAY DIFFRACTIONr_scbond_other2.7082.341898
X-RAY DIFFRACTIONr_scangle_it4.2073.4032780
X-RAY DIFFRACTIONr_scangle_other4.2063.4032781
X-RAY DIFFRACTIONr_lrange_it6.10926.334596
X-RAY DIFFRACTIONr_lrange_other5.90125.2814409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9290.321600.3063239X-RAY DIFFRACTION95.9898
1.929-1.9820.2511550.2233272X-RAY DIFFRACTION100
1.982-2.0390.2351480.1983217X-RAY DIFFRACTION100
2.039-2.1020.2251650.2073136X-RAY DIFFRACTION99.9092
2.102-2.1710.1891550.1562969X-RAY DIFFRACTION100
2.171-2.2470.2111800.1832914X-RAY DIFFRACTION99.9354
2.247-2.3320.2161470.152827X-RAY DIFFRACTION100
2.332-2.4270.1851620.1432692X-RAY DIFFRACTION99.965
2.427-2.5350.1831490.1322593X-RAY DIFFRACTION100
2.535-2.6590.2031260.1352505X-RAY DIFFRACTION99.962
2.659-2.8020.1991170.132377X-RAY DIFFRACTION100
2.802-2.9720.2031220.1362265X-RAY DIFFRACTION100
2.972-3.1770.1881150.1412140X-RAY DIFFRACTION100
3.177-3.4310.1891200.1461979X-RAY DIFFRACTION100
3.431-3.7580.1951130.1411822X-RAY DIFFRACTION99.9483
3.758-4.2010.199900.1251678X-RAY DIFFRACTION99.9435
4.201-4.8480.136890.1121501X-RAY DIFFRACTION100
4.848-5.9340.148750.1461269X-RAY DIFFRACTION100
5.934-8.3720.212480.1621025X-RAY DIFFRACTION100
8.372-46.110.22340.193613X-RAY DIFFRACTION99.5385

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