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- PDB-3a71: High resolution structure of Penicillium chrysogenum alpha-L-arab... -

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Basic information

Entry
Database: PDB / ID: 3a71
TitleHigh resolution structure of Penicillium chrysogenum alpha-L-arabinanase
ComponentsExo-arabinanase
KeywordsHYDROLASE / ARABINASE / GLYCOSYL HYDROLASE
Function / homologyNeuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta / ACETATE ION / Exo-arabinanase
Function and homology information
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.14 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Exo-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7735
Polymers39,3601
Non-polymers4144
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.877, 77.248, 79.441
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: UNP 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 52.81 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9794, 0.9700
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2006
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MO / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.971
ReflectionResolution: 1.14→10 Å / Num. obs: 149407 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 32
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.4 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.14→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / Num. parameters: 30027 / Num. restraintsaints: 36027 / SU B: 0.338 / SU ML: 0.017 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1283 7459 5.267 %RANDOM
obs0.1067 141611 94.7 %-
all-141611 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.17 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: 3336
FreeObs
Luzzati coordinate error0.017 Å0.029 Å
Luzzati sigma a0.338 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.14→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 28 537 3336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0336
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.133
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.095
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 572 -
Rwork0.194 10193 -
obs--98.11 %

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