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- PDB-1pp4: The crystal structure of rhamnogalacturonan acetylesterase in spa... -

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Basic information

Entry
Database: PDB / ID: 1pp4
TitleThe crystal structure of rhamnogalacturonan acetylesterase in space group P3121
ComponentsRhamnogalacturonan acetylesterase
KeywordsHYDROLASE / GDS(L) 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMolgaard, A. / Larsen, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase.
Authors: Molgaard, A. / Larsen, S.
#1: 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.
#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.F. / Kauppinen, S. / Dalboge, H. / Johnsen, A.H. / Poulsen, J.C.N. / Larsen, S.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1995
Title: Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus. Synergism between rhamnogalacturonan degrading enzymes
Authors: Kauppinen, S. / Christgau, S. / Kofod, L.V. / Halkier, T. / Dorreich, K. / Dalboge, H.
History
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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 1.5Aug 16, 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnogalacturonan acetylesterase
B: Rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1316
Polymers49,2462
Non-polymers8854
Water1,06359
1
A: Rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0653
Polymers24,6231
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhamnogalacturonan acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0653
Polymers24,6231
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.360, 75.360, 212.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer represented by either the A or the B chain in the asymmetric unit

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Components

#1: Protein Rhamnogalacturonan acetylesterase / RGAE


Mass: 24622.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: RHA1 / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): KSM 510
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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 4000, 2-propanol, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 15, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.6 Å / Num. all: 25036 / Num. obs: 24979 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 56.79 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.452 / % possible all: 93

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Processing

Software
NameVersionClassification
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1deo

1deo


Resolution: 2.5→28.18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.222 2413 10% chosen randomly
Rwork0.182 --
all-24979 -
obs-24456 -
Refinement stepCycle: LAST / Resolution: 2.5→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 56 59 3585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.306
LS refinement shellResolution: 2.5→2.61 Å /
RfactorNum. reflection
Rfree0.348 291
Rwork0.316 2657

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