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- PDB-2xhn: Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active ... -

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Basic information

Entry
Database: PDB / ID: 2xhn
TitleRhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant
ComponentsRHAMNOGALACTURONASE B
KeywordsLYASE / CARBOHYDRATE ACTIVE ENZYME / PECTIN / DEGRADATION / POLYSACCHARIDE LYASE FAMILY 4
Function / homology
Function and homology information


rhamnogalacturonan endolyase / rhamnogalacturonan endolyase activity / pectin catabolic process / cell wall organization / carbohydrate binding / extracellular region
Similarity search - Function
Rhamnogalacturonase B, N-terminal / Rhamnogalacturonase B / Rhamnogalacturonan lyase, domain III / Rhamnogalacturonan lyase, domain II / Rhamnogalacturonan lyase B, N-terminal / Polysaccharide lyase family 4, domain III / Polysaccharide lyase family 4, domain II / Carboxypeptidase-like, regulatory domain / Carbohydrate-binding-like fold / Beta-galactosidase; Chain A, domain 5 - #10 ...Rhamnogalacturonase B, N-terminal / Rhamnogalacturonase B / Rhamnogalacturonan lyase, domain III / Rhamnogalacturonan lyase, domain II / Rhamnogalacturonan lyase B, N-terminal / Polysaccharide lyase family 4, domain III / Polysaccharide lyase family 4, domain II / Carboxypeptidase-like, regulatory domain / Carbohydrate-binding-like fold / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Distorted Sandwich / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Rhamnogalacturonate lyase A
Similarity search - Component
Biological speciesASPERGILLUS ACULEATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsJensen, M.H. / Otten, H. / Christensen, U. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. / Lo Leggio, L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus Aculeatus.
Authors: Jensen, M.H. / Otten, H. / Christensen, U. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. / Leggio, L.L.
History
DepositionJun 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source
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.occupancy / _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] / _diffrn_source.pdbx_synchrotron_site
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHAMNOGALACTURONASE B
B: RHAMNOGALACTURONASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,28213
Polymers108,3712
Non-polymers91111
Water33,8681880
1
B: RHAMNOGALACTURONASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6106
Polymers54,1851
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: RHAMNOGALACTURONASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6727
Polymers54,1851
Non-polymers4866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.934, 108.978, 170.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-906-

SO4

21B-2281-

HOH

31B-2343-

HOH

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Components

#1: Protein RHAMNOGALACTURONASE B / RHAMNOGALACTURONAN LYASE / RGASE B / RHG B


Mass: 54185.422 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS ACULEATUS (mold) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: Q00019, pectin lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1880 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 169 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 169 TO ALA
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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: 20% PEG 4000, 0.1 AMMONIUM SULFATE, HANGING DROP VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2006 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
RadiationMonochromator: BENT SI (220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.52→20 Å / Num. obs: 142062 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 10.01 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 9.7 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NKG

1nkg


Resolution: 1.52→20.007 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 15.82 / Stereochemistry target values: ML
Details: RESIDUES GLN20, ASN435 AND THR493 ARE IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT IN BOTH CHAINS, BUT WELL SUPPORTED BY ELECTRON DENSITY AS IN THE NATIVE PDB 1NKG. THE LEU377 RESIDUE IS ...Details: RESIDUES GLN20, ASN435 AND THR493 ARE IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT IN BOTH CHAINS, BUT WELL SUPPORTED BY ELECTRON DENSITY AS IN THE NATIVE PDB 1NKG. THE LEU377 RESIDUE IS DISORDERED IN BOTH CHAINS.
RfactorNum. reflection% reflection
Rfree0.1644 7089 5 %
Rwork0.1133 --
obs0.1159 141887 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.768 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7352 Å20 Å20 Å2
2--1.3917 Å20 Å2
3---0.8692 Å2
Refinement stepCycle: LAST / Resolution: 1.52→20.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7622 0 46 1880 9548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098116
X-RAY DIFFRACTIONf_angle_d1.2411144
X-RAY DIFFRACTIONf_dihedral_angle_d11.4512875
X-RAY DIFFRACTIONf_chiral_restr0.0731263
X-RAY DIFFRACTIONf_plane_restr0.0061440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5202-1.53740.18322140.09284070X-RAY DIFFRACTION83
1.5374-1.55550.18312190.09514179X-RAY DIFFRACTION87
1.5555-1.57450.18912530.09334246X-RAY DIFFRACTION87
1.5745-1.59440.1952240.09844140X-RAY DIFFRACTION86
1.5944-1.61540.18472220.0914210X-RAY DIFFRACTION86
1.6154-1.63750.16922240.08714196X-RAY DIFFRACTION86
1.6375-1.66090.17092180.09124209X-RAY DIFFRACTION86
1.6609-1.68570.17032100.09364204X-RAY DIFFRACTION86
1.6857-1.7120.16362260.0934238X-RAY DIFFRACTION87
1.712-1.740.17192230.09774293X-RAY DIFFRACTION87
1.74-1.770.16482110.09594308X-RAY DIFFRACTION88
1.77-1.80220.16742150.09844364X-RAY DIFFRACTION89
1.8022-1.83680.18022360.10564492X-RAY DIFFRACTION91
1.8368-1.87430.17762280.10424506X-RAY DIFFRACTION92
1.8743-1.9150.17832560.10464497X-RAY DIFFRACTION93
1.915-1.95950.1612590.10394583X-RAY DIFFRACTION94
1.9595-2.00850.14422390.10274681X-RAY DIFFRACTION96
2.0085-2.06270.1672330.10224733X-RAY DIFFRACTION97
2.0627-2.12340.15742760.09864771X-RAY DIFFRACTION98
2.1234-2.19180.15412400.09654798X-RAY DIFFRACTION98
2.1918-2.27010.16532470.10684812X-RAY DIFFRACTION97
2.2701-2.36080.15672460.09884760X-RAY DIFFRACTION97
2.3608-2.46810.15032500.09874798X-RAY DIFFRACTION97
2.4681-2.59790.15392370.10864759X-RAY DIFFRACTION97
2.5979-2.76030.1682420.10864731X-RAY DIFFRACTION96
2.7603-2.97280.14692370.1124732X-RAY DIFFRACTION95
2.9728-3.27080.15432550.12124663X-RAY DIFFRACTION95
3.2708-3.74140.16022570.12054650X-RAY DIFFRACTION93
3.7414-4.70370.1262440.10814609X-RAY DIFFRACTION92
4.7037-20.00820.16242480.13974566X-RAY DIFFRACTION88

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