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- PDB-1k7c: Rhamnogalacturonan acetylesterase with seven N-linked carbohydrat... -

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Basic information

Entry
Database: PDB / ID: 1k7c
TitleRhamnogalacturonan acetylesterase with seven N-linked carbohydrate residues distributed at two N-glycosylation sites refined at 1.12 A resolution
Componentsrhamnogalacturonan acetylesterase
KeywordsHYDROLASE / N-linked glycosylation / SGNH-hydrolase
Function / homology
Function and homology information


rhamnogalacturonan acetylesterase / hydrolase activity, acting on ester bonds
Similarity search - Function
Rhamnogalacturonan acetylesterase RhgT-like / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Rhamnogalacturonan acetylesterase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.12 Å
AuthorsMolgaard, A. / Larsen, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A branched N-linked glycan at atomic resolution in the 1.12 A structure of rhamnogalacturonan acetylesterase.
Authors: Molgaard, A. / Larsen, S.
#1: Journal: To be Published
Title: Rhamnogalacturonan acetylesterase, a member of the SGNH-hydrolase family.
Authors: Molgaard, A.
#2: Journal: Structure / Year: 2000
Title: Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
Authors: Molgaard, A. / Kauppinen, S. / Larsen, S.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of the heterogeneously glycosylated enzyme rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
Authors: Molgaard, A. / Petersen, J.F.W. / Kauppinen, S. / Dalboge, H. / Johnsen, A.H. / Poulsen, J.-C.N. / Larsen, S.
#4: Journal: J.Biol.Chem. / Year: 1995
Title: Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
Authors: Kauppinen, S. / Christgau, S. / Kofod, L.V. / Halkier, T. / Dorreich, K. / Dalboge, H.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / software / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3017
Polymers24,6231
Non-polymers1,6786
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.170, 56.920, 71.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rhamnogalacturonan acetylesterase


Mass: 24622.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): A1560 / References: GenBank: 1004217, UniProt: Q00017*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 329 / 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: 1.85 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Li2SO4, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Molgaard, A., (1998) Acta Crystallogr., Sect.D, 54, 1026.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.4 M1reservoiror 1.4M (NH4)2SO4Li2SO4
20.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1024 / Wavelength: 1.1024 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1024 Å / Relative weight: 1
ReflectionResolution: 1.12→38 Å / Num. all: 644629 / Num. obs: 644629 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 0.37 / % possible all: 82.1
Reflection
*PLUS
Num. obs: 80624 / Num. measured all: 644629 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 82.1 % / Rmerge(I) obs: 0.37

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIR
Starting model: 1DEO

1deo


Resolution: 1.12→40 Å / Num. parameters: 19970 / Num. restraintsaints: 24756 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1344 4019 5 %RANDOM
Rwork0.1033 ---
all0.1095 80568 --
obs0.1045 71116 97.8 %-
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 1706 / Occupancy sum non hydrogen: 2123.96
Refinement stepCycle: LAST / Resolution: 1.12→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 106 329 2170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_from_restr_planes0.0264
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.195
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.022
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 38 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.11 / Rfactor obs: 0.103 / Rfactor Rfree: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.026
X-RAY DIFFRACTIONs_chiral_restr0.079

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