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- PDB-3a72: High resolution structure of Penicillium chrysogenum alpha-L-arab... -

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Basic information

Entry
Database: PDB / ID: 3a72
TitleHigh resolution structure of Penicillium chrysogenum alpha-L-arabinanase complexed with arabinobiose
ComponentsExo-arabinanase
KeywordsHYDROLASE / ARABINASE / GLYCOSYL HYDROLASE
Function / homologyNeuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta / Exo-arabinanase
Function and homology information
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsSogabe, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: High-resolution structure of exo-arabinanase from Penicillium chrysogenum
Authors: Sogabe, Y. / Kitatani, T. / Yamaguchi, A. / Kinoshita, T. / Adachi, H. / Takano, K. / Inoue, T. / Mori, Y. / Matsumura, H. / Sakamoto, T. / Tada, T.
History
DepositionSep 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6422
Polymers39,3601
Non-polymers2821
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.959, 77.117, 79.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exo-arabinanase / EXO-1 / 5-ALPHA-L-ARABINANASE


Mass: 39359.625 Da / Num. of mol.: 1 / Fragment: Residues 24-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Strain: 31B / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: Q7ZA77, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a211h-1a_1-4]/1-1/a5-b1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 277 K / pH: 4.5
Details: 28% MPD, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 24, 2006
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.04→10 Å / Num. obs: 196659 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.5
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A71

3a71


Resolution: 1.04→10 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.964 / Num. parameters: 30063 / Num. restraintsaints: 36062 / SU B: 0.247 / SU ML: 0.013 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1254 9813 5.263 %RANDOM
obs0.1044 186439 94.7 %-
all-186439 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2652 / Occupancy sum non hydrogen: 3340
FreeObs
Luzzati coordinate error0.013 Å0.023 Å
Luzzati sigma a0.247 Å0.024 Å
Refinement stepCycle: LAST / Resolution: 1.04→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 19 546 3336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0343
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.155
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.108
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 672 -
Rwork0.247 13407 -
obs--97.72 %

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