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- PDB-4bf7: Emericilla nidulans endo-beta-1,4-galactanase -

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Basic information

Entry
Database: PDB / ID: 4bf7
TitleEmericilla nidulans endo-beta-1,4-galactanase
ComponentsARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A
KeywordsHYDROLASE
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / cell wall organization / extracellular region
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Arabinogalactan endo-beta-1,4-galactanase A
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsOtten, H. / Michalak, M. / Larsen, S. / Mikkelsen, J.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Binding of Zinc Ions to Emericella Nidulans Endo-[Beta]-1,4-Galactanase is Essential for Crystal Formation
Authors: Otten, H. / Michalak, M. / Mikkelsen, J.D. / Larsen, S.
History
DepositionMar 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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 1.4May 8, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,75030
Polymers38,7371
Non-polymers2,01329
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 72.370, 98.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A / ENDO-1 / 4-BETA-GALACTANASE A / GALACTANASE A / ENDO-BETA-1 / 4-GALACTANASE


Mass: 38736.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SULFIDE BRIDGES BETWEEN A C253-C310
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Production host: KOMAGATAELLA PASTORIS (fungus)
References: UniProt: Q5B153, arabinogalactan endo-beta-1,4-galactanase
#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 / N-Acetylglucosamine


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

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Non-polymers , 5 types, 209 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFUNGAL GENETICS STOCK CENTER

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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 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growpH: 8
Details: 200 MM ZN ACETATE, 100 MM IMIDAZOLE, 20%(W/V) PEG 3000, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2012
Details: ONE PAIR OF PT COATED SI FOCUSING MIRRORS, KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY DIFFRACTING SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→47 Å / Num. obs: 58261 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOB

1fob


Resolution: 2.001→47.475 Å / SU ML: 0.18 / σ(F): 1.21 / Phase error: 17.04 / Stereochemistry target values: ML
Details: N-TERMINAL 1-17 MILSSLLPLSLVTLTSA IS DISORDERED AND NOT MODELLED
RfactorNum. reflection% reflection
Rfree0.1923 2912 5 %
Rwork0.1575 --
obs0.1592 58202 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.001→47.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 84 181 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112755
X-RAY DIFFRACTIONf_angle_d1.2473757
X-RAY DIFFRACTIONf_dihedral_angle_d13.667947
X-RAY DIFFRACTIONf_chiral_restr0.082415
X-RAY DIFFRACTIONf_plane_restr0.005493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0012-2.0340.32051210.25452346X-RAY DIFFRACTION90
2.034-2.06910.23491400.22212668X-RAY DIFFRACTION100
2.0691-2.10670.24341430.20262660X-RAY DIFFRACTION100
2.1067-2.14730.19721390.18472616X-RAY DIFFRACTION100
2.1473-2.19110.21671410.17432674X-RAY DIFFRACTION100
2.1911-2.23870.20371380.16432639X-RAY DIFFRACTION100
2.2387-2.29080.18181420.16812648X-RAY DIFFRACTION100
2.2908-2.34810.19641430.16472637X-RAY DIFFRACTION100
2.3481-2.41160.2011390.15352660X-RAY DIFFRACTION100
2.4116-2.48250.19221320.1382612X-RAY DIFFRACTION100
2.4825-2.56270.15961390.13362629X-RAY DIFFRACTION100
2.5627-2.65420.2251420.13142712X-RAY DIFFRACTION100
2.6542-2.76050.16891340.13462616X-RAY DIFFRACTION100
2.7605-2.88610.1731400.13162634X-RAY DIFFRACTION100
2.8861-3.03830.17881400.13522672X-RAY DIFFRACTION100
3.0383-3.22860.16971430.1382626X-RAY DIFFRACTION100
3.2286-3.47780.16951420.13832650X-RAY DIFFRACTION100
3.4778-3.82760.18731440.13742659X-RAY DIFFRACTION100
3.8276-4.38120.17171340.13312629X-RAY DIFFRACTION100
4.3812-5.51850.18261320.1572662X-RAY DIFFRACTION100
5.5185-47.48790.21721440.2162641X-RAY DIFFRACTION100

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