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

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Basic information

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


acetylesterase / polysaccharide metabolic process / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetyl xylan esterase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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)435,89149
Polymers433,37812
Non-polymers2,51337
Water32,2831792
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)217,88524
Polymers216,6896
Non-polymers1,19618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21110 Å2
ΔGint-170 kcal/mol
Surface area63850 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)218,00625
Polymers216,6896
Non-polymers1,31619
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21390 Å2
ΔGint-160 kcal/mol
Surface area63840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.485, 167.686, 144.961
Angle α, β, γ (deg.)90.000, 91.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHILMN

#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

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Non-polymers , 6 types, 1829 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1792 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.2M 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: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2002
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→29.9 Å / Num. all: 135665 / Num. obs: 135665 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 34.36 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1
Reflection shellResolution: 2.5→2.51 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5110 / Χ2: 0.883 / % possible all: 93.4

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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: 2.5→29.9 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 839462 / 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
Rfree0.228 13527 10 %RANDOM
Rwork0.184 ---
all0.184 135607 --
obs0.184 135607 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.294 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 18.658 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20.72 Å2
2--0.79 Å20 Å2
3---0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30522 0 134 1792 32448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 2254 10.2 %
Rwork0.239 19951 -
all-22205 -
obs--92.9 %
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
X-RAY DIFFRACTION6PEG.PARPEG.TOP
X-RAY DIFFRACTION7PGE.PARPGE.TOP
X-RAY DIFFRACTION8PG4.PARPG4.TOP

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