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- PDB-3njx: Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A -

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Basic information

Entry
Database: PDB / ID: 3njx
TitleRhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A
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 / MOLECULAR REPLACEMENT / Resolution: 1.94 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. / Larsen, S. / Leggio, L.L.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnogalacturonase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6016
Polymers54,1761
Non-polymers4245
Water13,061725
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.071, 77.071, 171.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsmonomer

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Components

#1: Protein Rhamnogalacturonase B / Rhamnogalacturonan lyase / RGase B / RHG B


Mass: 54176.457 Da / Num. of mol.: 1 / Fragment: Rhamnogalacturonase B, residues 20-527 / Mutation: H210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: rhgB / Production host: Aspergillus oryzae (mold) / References: UniProt: Q00019, pectin lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 20% PEG4000, 0.1 M Ammonium Sulphate with 9% PEG400 as cryo protectant, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 30, 2005 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→70 Å / Num. obs: 35438 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 6.8 / Rsym value: 0.305 / % possible all: 90.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NKG

1nkg


Resolution: 1.94→19.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.887 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1766 5 %RANDOM
Rwork0.167 ---
obs0.169 33629 91 %-
all-33629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 21 725 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.9365354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15923.625160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0591519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1680.21775
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22656
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2341.52586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41724059
X-RAY DIFFRACTIONr_scbond_it0.6131560
X-RAY DIFFRACTIONr_scangle_it0.8734.51295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 129 -
Rwork0.184 2305 -
obs--86.74 %

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