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- PDB-2vxk: Structural comparison between Aspergillus fumigatus and human GNA1 -

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Basic information

Entry
Database: PDB / ID: 2vxk
TitleStructural comparison between Aspergillus fumigatus and human GNA1
ComponentsGLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE
KeywordsTRANSFERASE / KINETICS / UDP-GLCNAC / INHIBITOR DESIGN
Function / homology
Function and homology information


glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-16G / COENZYME A / PHOSPHATE ION / Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHurtado-Guerrero, R. / Raimi, O.G. / Min, J. / Zeng, H. / Vallius, L. / Shepherd, S. / Ibrahim, A.F.M. / Wu, H. / Plotnikov, A.N. / van Aalten, D.M.F.
CitationJournal: Biochem.J. / Year: 2008
Title: Structural and Kinetic Differences between Human and Aspergillus Fumigatus D-Glucosamine-6- Phosphate N-Acetyltransferase.
Authors: Hurtado-Guerrero, R. / Raimi, O.G. / Min, J. / Zeng, H. / Vallius, L. / Shepherd, S. / Ibrahim, A.F.M. / Wu, H. / Plotnikov, A.N. / Van Aalten, D.M.F.
History
DepositionJul 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2904
Polymers21,1261
Non-polymers1,1643
Water2,594144
1
A: GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE
hetero molecules

A: GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5808
Polymers42,2522
Non-polymers2,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9060 Å2
ΔGint-37 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.606, 100.826, 55.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE / AFGNA1


Mass: 21126.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q4WCU5, glucosamine-phosphate N-acetyltransferase
#2: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.27 % / Description: NONE

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Data collection

DiffractionMean temperature: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 18376 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 10.5 / % possible all: 98

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.622 / SU ML: 0.081 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA IS NOT COMPLETE MODELLED SINCE AT THE END OF THE MOLECULE (REGION OF THE THIOL GROUP) WAS COMPLETELY DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 582 3.2 %RANDOM
Rwork0.178 ---
obs0.179 17780 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 65 144 1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221526
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5462.0352105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.12523.62369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5081512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021139
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2691
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21043
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8481.5893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24821431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2443720
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4814.5655
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 45
Rwork0.204 1282
Refinement TLS params.Method: refined / Origin x: -26.385 Å / Origin y: -18.1102 Å / Origin z: -4.2609 Å
111213212223313233
T-0.0931 Å20.0043 Å2-0.0208 Å2--0.0819 Å2-0.007 Å2---0.0861 Å2
L1.6215 °2-0.1085 °20.3115 °2-1.6659 °2-0.2146 °2--1.7675 °2
S-0.0345 Å °-0.0952 Å °-0.0224 Å °0.1196 Å °-0.0364 Å °-0.0037 Å °-0.058 Å °-0.077 Å °0.071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 190
2X-RAY DIFFRACTION1A1191
3X-RAY DIFFRACTION1A1192
4X-RAY DIFFRACTION1A1193
5X-RAY DIFFRACTION1A2001 - 2144

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