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- PDB-3fvt: Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus,... -

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Basic information

Entry
Database: PDB / ID: 3fvt
TitleCrystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus
Function / homology
Function and homology information


acetylesterase / acetylesterase activity
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl xylan esterase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKrastanova, I. / Cassetta, A. / Lamba, D.
Citation
Journal: To be Published
Title: Structural and functional studies of Bacillus pumilus acetyl xylan esterase
Authors: Krastanova, I. / Cassetta, A. / Mastihubova, M. / Biely, P. / Lamba, D.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Heterologous expression, purification, crystallization, X-ray analysis and phasing of the acetyl xylan esterase from Bacillus pumilus
Authors: Krastanova, I. / Guarnaccia, C. / Zahariev, S. / Degrassi, G. / Lamba, D.
#2: Journal: Microbiology / Year: 2000
Title: The acetyl xylan esterase of Bacillus pumilus belongs to a family of esterases with broad substrate specificity
Authors: Degrassi, G. / Kojic, M. / Ljubijankic, G. / Venturi, V.
#3: Journal: Appl.Environ.Microbiol. / Year: 1998
Title: Purification and characterization of an acetyl xylan esterase from Bacillus pumilus
Authors: Degrassi, G. / Okeke, B.C. / Bruschi, C.V. / Venturi, V.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Acetyl xylan esterase
B: Acetyl xylan esterase
C: Acetyl xylan esterase
D: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
G: Acetyl xylan esterase
H: Acetyl xylan esterase
I: Acetyl xylan esterase
L: Acetyl xylan esterase
M: Acetyl xylan esterase
N: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,41338
Polymers433,37812
Non-polymers1,03526
Water56,7833152
1
A: Acetyl xylan esterase
B: Acetyl xylan esterase
C: Acetyl xylan esterase
D: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,20719
Polymers216,6896
Non-polymers51813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18940 Å2
ΔGint-177 kcal/mol
Surface area63980 Å2
MethodPISA
2
G: Acetyl xylan esterase
H: Acetyl xylan esterase
I: Acetyl xylan esterase
L: Acetyl xylan esterase
M: Acetyl xylan esterase
N: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,20719
Polymers216,6896
Non-polymers51813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-183 kcal/mol
Surface area64150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.039, 87.205, 184.825
Angle α, β, γ (deg.)90.000, 112.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl xylan esterase


Mass: 36114.844 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: modified pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3152 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.5M lithium chloride, 5% PEG 6000, 0.1M MES, pH 6.0, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.278 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2002
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.9→29.75 Å / Num. all: 298796 / Num. obs: 298796 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.116
Reflection shellResolution: 1.9→1.91 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2 / Num. unique all: 9621 / Χ2: 1 / % possible all: 80.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
MAR345controldata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ODS

1ods


Resolution: 1.9→29.74 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 960989 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 29799 10 %RANDOM
Rwork0.211 ---
all0.211 298450 --
obs0.211 298450 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.807 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 64.62 Å2 / Biso mean: 22.086 Å2 / Biso min: 2.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20.61 Å2
2---0.76 Å20 Å2
3---2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30462 0 36 3152 33650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.952
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 4365 9.9 %
Rwork0.24 39737 -
all-44102 -
obs--80.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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