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- PDB-1fob: CRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEA... -

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Basic information

Entry
Database: PDB / ID: 1fob
TitleCRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEATUS AT 100K
ComponentsBETA-1,4-GALACTANASE
KeywordsHYDROLASE / B/A barrel / glycosyl hydrolase / family 53 / clan GH-A
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity
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
Arabinogalactan endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRyttersgaard, C. / Larsen, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Aspergillus aculeatus beta-1,4-Galactanase: Substrate Recognition and Relations to Other Glycoside Hydrolases in Clan GH-A
Authors: Ryttersgaard, C. / Leggio, L.L. / Coutinho, P.M. / Henrissat, B. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Studies of beta-1,4-galactanase from Aspergillus aculeatus
Authors: Ryttersgaard, C. / Poulsen, J. / Christgau, S. / Sandal, T. / Dalboge, H. / Larsen, S.
History
DepositionAug 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: BETA-1,4-GALACTANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8162
Polymers36,7751
Non-polymers401
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.700, 87.980, 128.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein BETA-1,4-GALACTANASE


Mass: 36775.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus aculeatus (mold)
References: UniProt: P48842, arabinogalactan endo-beta-1,4-galactanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, calcium chloride, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Ryttersgaard, C., (1999) Acta Crystallogr.,Sect.D, 55, 929.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(v/v)PEG4001reservoir
20.2 M1reservoirCaCl2
30.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0874
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0874 Å / Relative weight: 1
ReflectionResolution: 1.8→28.59 Å / Num. all: 31237 / Num. obs: 31237 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Num. unique all: 1477 / % possible all: 91.4
Reflection shell
*PLUS
Lowest resolution: 1.83 Å / % possible obs: 97.7 % / Mean I/σ(I) obs: 66.6

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.8→28.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2119317.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1576 5 %RANDOM
Rwork0.211 ---
all0.211 31237 --
obs0.211 31237 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.01 Å2 / ksol: 0.3744 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---2.82 Å20 Å2
3---2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 1 193 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 249 5.2 %
Rwork0.271 4522 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.252 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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