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- PDB-2ixb: Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC -

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Basic information

Entry
Database: PDB / ID: 2ixb
TitleCrystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC
ComponentsALPHA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / N-ACETYLGALACTOSAMINIDASE / NAD / A-ECO CONVERSION
Function / homology
Function and homology information


alpha-N-acetylgalactosaminidase / alpha-N-acetylgalactosaminidase activity / metabolic process / nucleotide binding
Similarity search - Function
: / Glycosyl hydrolase 109, C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...: / Glycosyl hydrolase 109, C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesFLAVOBACTERIUM MENINGOSEPTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSulzenbacher, G. / Liu, Q.P. / Bourne, Y. / Henrissat, B. / Clausen, H.
CitationJournal: Nat.Biotechnol. / Year: 2007
Title: Bacterial Glycosidases for the Production of Universal Red Blood Cells.
Authors: Liu, Q.P. / Sulzenbacher, G. / Yuan, H. / Bennett, E.P. / Pietz, G. / Saunders, K. / Spence, J. / Nudelman, E. / Levery, S.B. / White, T. / Neveu, J.M. / Lane, W.S. / Bourne, Y. / Olsson, M. ...Authors: Liu, Q.P. / Sulzenbacher, G. / Yuan, H. / Bennett, E.P. / Pietz, G. / Saunders, K. / Spence, J. / Nudelman, E. / Levery, S.B. / White, T. / Neveu, J.M. / Lane, W.S. / Bourne, Y. / Olsson, M.L. / Henrissat, B. / Clausen, H.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5216
Polymers50,2821
Non-polymers1,2395
Water3,207178
1
A: ALPHA-N-ACETYLGALACTOSAMINIDASE
hetero molecules

A: ALPHA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04212
Polymers100,5632
Non-polymers2,47810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)88.189, 88.189, 301.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ALPHA-N-ACETYLGALACTOSAMINIDASE /


Mass: 50281.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FLAVOBACTERIUM MENINGOSEPTICUM (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: A4Q8F7*PLUS, alpha-N-acetylgalactosaminidase
#3: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 182 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.44 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.25
Details: 46-50% 2-METHYL-2,4-PENTANEDIOL (MPD), 75 MM NA-CITRATE PH 6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 27626 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 43.94 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.4 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IXA

2ixa


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.727 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GLOBAL B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1111 4.1 %RANDOM
Rwork0.173 ---
obs0.174 26303 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å21.43 Å20 Å2
2--2.85 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 83 178 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213601
X-RAY DIFFRACTIONr_bond_other_d0.0010.022456
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.954875
X-RAY DIFFRACTIONr_angle_other_deg0.8535956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97824.278180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31315607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4961520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
X-RAY DIFFRACTIONr_nbd_refined0.180.2689
X-RAY DIFFRACTIONr_nbd_other0.190.22516
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21697
X-RAY DIFFRACTIONr_nbtor_other0.0830.21782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.52748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49123387
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91131800
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3864.51486
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 61
Rwork0.285 1413
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.32550.33260.03531.96670.55573.2102-0.06850.4095-0.214-0.36070.0038-0.07290.3616-0.15650.06470.0482-0.05990.10250.0461-0.1129-0.0493-11.330745.2454-9.2204
20.7180.06010.11031.8272-0.07531.9355-0.04480.16-0.0366-0.07140.0107-0.1528-0.050.10450.0341-0.1644-0.01740.0358-0.09470.0114-0.1281-7.683860.259110.5956
32.93060.32590.52861.64060.16574.3440.01950.1023-0.554-0.04320.06390.04320.9871-0.2703-0.08340.1619-0.09260.0856-0.0753-0.03310.0963-18.783133.563914.0668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 128
2X-RAY DIFFRACTION2A129 - 167
3X-RAY DIFFRACTION2A206 - 238
4X-RAY DIFFRACTION2A266 - 429
5X-RAY DIFFRACTION3A168 - 205
6X-RAY DIFFRACTION3A239 - 265

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