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- PDB-1deo: RHAMNOGALACTURONAN ACETYLESTERASE FROM ASPERGILLUS ACULEATUS AT 1... -

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Basic information

Entry
Database: PDB / ID: 1deo
TitleRHAMNOGALACTURONAN ACETYLESTERASE FROM ASPERGILLUS ACULEATUS AT 1.55 A RESOLUTION WITH SO4 IN THE ACTIVE SITE
ComponentsRHAMNOGALACTURONAN ACETYLESTERASE
KeywordsHYDROLASE / 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 / Resolution: 1.55 Å
AuthorsMolgaard, A. / Kauppinen, S. / Larsen, S.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
Authors: Molgaard, A. / Kauppinen, S. / Larsen, S.
#1: 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.
#2: 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. / Kauppinen, S. / Dalboge, H. / Johnsen, A. / Navarro Poulsen, J.-C. / Larsen, S.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)26,1095
Polymers24,6231
Non-polymers1,4864
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.14, 56.87, 71.89
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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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) / Strain: KSM 510 / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): A1560 / References: EMBL: Q00017, UniProt: Q00017*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-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]DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3-3/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)][b-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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Lithium sulfate, Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 M11Li2SO4
20.1 Msodium acetate11
340 OD280protein11

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 25, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 28693 / Num. obs: 28693 / % possible obs: 91 % / Redundancy: 7.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.293 / Num. unique all: 3517 / % possible all: 77.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 77.9 %

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Processing

Software
NameVersionClassification
ROTAVATAdata reduction
MLPHAREphasing
X-PLOR3.851refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.55→30 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2818 -10% chosen randomly
Rwork0.164 ---
all-28647 --
obs-28316 98.7 %-
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 96 153 1984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.6
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.164 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3

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