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- PDB-3c1u: D192N mutant of Rhamnogalacturonan acetylesterase -

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Basic information

Entry
Database: PDB / ID: 3c1u
TitleD192N mutant of Rhamnogalacturonan acetylesterase
ComponentsRhamnogalacturonan acetylesterase
KeywordsHYDROLASE / SGNH hydrolase / pectin degradation / Glycoprotein
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
ACETATE ION / Rhamnogalacturonan acetylesterase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLangkilde, A. / Lo Leggio, L. / Navarro Poulsen, J.C. / Molgaard, A. / Larsen, S.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2008
Title: Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase
Authors: Langkilde, A. / Kristensen, S.M. / Lo Leggio, L. / Jensen, J.H. / Houk, A.R. / Navarro Poulsen, J.C. / Kauppinen, S. / Larsen, S.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase
Authors: Molgaard, A. / Larsen, S.
#2: 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.
#3: 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.
#4: 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. / Navarro Poulsen, J.C. / Larsen, S.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1234
Polymers24,6221
Non-polymers5013
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.612, 67.606, 73.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rhamnogalacturonan acetylesterase / RGAE


Mass: 24621.895 Da / Num. of mol.: 1 / Mutation: D192N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: rha1 / Plasmid: pHD464 / Production host: Aspergillus oryzae (mold)
References: UniProt: Q00017, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: 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.: 2
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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.45 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: PEG1500, sodium acetate, pH3.0, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→20 Å / Num. all: 55818 / Num. obs: 55818 / % possible obs: 99.5 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 31.8
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.198 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.004data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K7C

1k7c


Resolution: 1.33→20 Å / Num. parameters: 19411 / Num. restraintsaints: 23615 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: One loop was very poorly defined in the electron density maps and as a consequence SER78 and THR81 are only modelled with an occupancy of 0.5. LEU79 and SER80 could not be positioned in the ...Details: One loop was very poorly defined in the electron density maps and as a consequence SER78 and THR81 are only modelled with an occupancy of 0.5. LEU79 and SER80 could not be positioned in the maps and are therefore not included in the model. The geometry and position of this loop is inflicted with higher uncertainty.
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2793 5 %RANDOM
Rwork0.114 ---
obs0.115 55818 99.4 %-
all-55818 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 18.464 Å2
Refinement stepCycle: LAST / Resolution: 1.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 32 355 2108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.107

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