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- PDB-4zm6: A unique GCN5-related glucosamine N-acetyltransferase region exis... -

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Basic information

Entry
Database: PDB / ID: 4zm6
TitleA unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain GH3 beta-N-acetylglucosaminidase
ComponentsN-acetyl-beta-D glucosaminidase
KeywordsHYDROLASE / TRANSFERASE / beta-N-acetylglucosaminidase / glucosamine N-acetyltransferase / glycoside hydrolase family 3
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / peptidoglycan turnover / acyltransferase activity, transferring groups other than amino-acyl groups / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase ...: / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyl-beta-D glucosaminidase
Similarity search - Component
Biological speciesRhizomucor miehei CAU432 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsQin, Z. / Xiao, Y. / Yang, X. / Jiang, Z. / Yang, S. / Mesters, J.R.
CitationJournal: Sci Rep / Year: 2015
Title: A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 beta-N-acetylglucosaminidase
Authors: Qin, Z. / Xiao, Y. / Yang, X. / Mesters, J.R. / Yang, S. / Jiang, Z.
History
DepositionMay 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: N-acetyl-beta-D glucosaminidase
B: N-acetyl-beta-D glucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,6777
Polymers192,7702
Non-polymers1,9075
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-56 kcal/mol
Surface area64870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.034, 245.034, 94.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

21B-1011-

HOH

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Components

#1: Protein N-acetyl-beta-D glucosaminidase / beta-N-acetylglucosaminidase / glucosamine N-acetyltransferase


Mass: 96384.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei CAU432 (fungus) / Strain: CAU432 / Gene: Nag / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: V9M3A9, beta-N-acetylhexosaminidase, EC: 2.3.1.3
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.3-1.6 M (NH4)2SO4 , 0.1 M Bis-Tris pH 5.5-6.5 / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0331 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.8→88.19 Å / Num. obs: 71082 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.0118 / Net I/σ(I): 29.4
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 4.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata processing
PHASERphasing
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→86.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.688 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.661 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25404 3440 4.9 %RANDOM
Rwork0.22917 ---
obs0.23039 66951 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→86.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 117 114 13446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01913608
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212965
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.96218495
X-RAY DIFFRACTIONr_angle_other_deg0.719329732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61851688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42424.436629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49152271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8811582
X-RAY DIFFRACTIONr_chiral_restr0.0560.22067
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023138
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0486.7026759
X-RAY DIFFRACTIONr_mcbond_other2.0486.7026756
X-RAY DIFFRACTIONr_mcangle_it3.4710.058443
X-RAY DIFFRACTIONr_mcangle_other3.4710.058444
X-RAY DIFFRACTIONr_scbond_it1.666.8096849
X-RAY DIFFRACTIONr_scbond_other1.6566.8036838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.90210.13510035
X-RAY DIFFRACTIONr_long_range_B_refined5.48652.45715068
X-RAY DIFFRACTIONr_long_range_B_other5.48652.45715068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 252 -
Rwork0.325 4858 -
obs--98.61 %

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