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

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Basic information

Entry
Database: PDB / ID: 6vva
TitleN-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300)
ComponentsN-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / NanE / TIM-barrel / epimerase
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 / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsRenwick, R.C.J. / Currie, M.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
DepositionFeb 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 11, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _software.classification / _software.name / _software.version / _struct_keywords.text
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 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 2.2Oct 11, 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

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Assembly

Deposited unit
A: N-acetylmannosamine-6-phosphate 2-epimerase
B: N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5976
Polymers49,1422
Non-polymers4554
Water10,539585
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area20250 Å2
Unit cell
Length a, b, c (Å)44.431, 77.067, 173.745
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, UniProt: Q2G157*PLUS, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
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: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→46.34 Å / Num. obs: 52642 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.995 / Net I/σ(I): 10.8
Reflection shellResolution: 1.84→1.906 Å / Num. unique obs: 5094 / CC1/2: 0.592

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y0E

1y0e


Resolution: 1.84→46.34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.021 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1993 3.8 %RANDOM
Rwork0.1797 ---
obs0.1807 50648 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.6 Å2 / Biso mean: 16.312 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---0.98 Å2
Refinement stepCycle: final / Resolution: 1.84→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 28 585 4053
Biso mean--33.06 30.62 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173674
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.6385192
X-RAY DIFFRACTIONr_angle_other_deg1.0991.5818526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70324.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73915699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0211517
X-RAY DIFFRACTIONr_chiral_restr0.0410.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 142 -
Rwork0.305 3618 -
all-3760 -
obs--98.51 %

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