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- PDB-3fcy: Crystal Structure of Acetyl Xylan Esterase 1 from Thermoanaerobac... -

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Basic information

Entry
Database: PDB / ID: 3fcy
TitleCrystal Structure of Acetyl Xylan Esterase 1 from Thermoanaerobacterium sp. JW/SL YS485
ComponentsXylan esterase 1
KeywordsHYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Thermoanaerobacterium sp.
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
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
Biological speciesThermoanaerobacterium sp. 'JW/SL YS485' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKrastanova, I. / Cassetta, A. / Lamba, D.
Citation
Journal: To be Published
Title: Crystal Structure Analysis of Acetyl Xylan Esterase 1 from Thermoanaerobacterium sp. JW/SL YS485
Authors: Krastanova, I. / Cassetta, A. / Wiegel, J. / Lamba, D.
#1: Journal: APPL.ENVIRON.MICROBIOL. / Year: 1995
Title: Purification and Characterization of Two Thermostable Acetyl Xylan Esterases from Thermoanaerobacterium sp. Strain JW/SL-YS485
Authors: Shao, W. / Wiegel, J.
#2: Journal: J.BACTERIOL. / Year: 1997
Title: Isolation, Analysis, and Expression of Two Genes from Thermoanaerobacterium sp. Strain JW/SL YS485: a beta-Xylosidase and a Novel Acetyl Xylan Esterase with Cephalosporin C Deacetylase Activity
Authors: Lorenz, W.W. / Wiegel, J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1955
Polymers118,1153
Non-polymers802
Water8,809489
1
A: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules

A: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,38910
Polymers236,2296
Non-polymers1604
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area15970 Å2
ΔGint-55 kcal/mol
Surface area60200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.263, 132.263, 112.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-321-

CA

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Components

#1: Protein Xylan esterase 1


Mass: 39371.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium sp. 'JW/SL YS485' (bacteria)
Strain: JW/SL YS485 / Gene: axe1 / Plasmid: modified pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: O30361, acetylxylan esterase, cephalosporin-C deacetylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 14% PEG 400, 0.1M calcium chloride, 0.05M sodium HEPES, pH 7.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 66742 / Num. obs: 66742 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.01
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3296 / Χ2: 0.972 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å25 Å
Translation3.5 Å25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FVR

3fvr


Resolution: 2.1→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6761 10.1 %RANDOM
Rwork0.184 ---
all0.184 66710 --
obs0.184 66710 100 %-
Solvent computationBsol: 53.972 Å2
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 28 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.705 Å20.702 Å20 Å2
2--2.705 Å20 Å2
3----5.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 2 489 8063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_mcbond_it1.1241.5
X-RAY DIFFRACTIONc_scbond_it1.9832
X-RAY DIFFRACTIONc_mcangle_it1.5842
X-RAY DIFFRACTIONc_scangle_it2.8942.5
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

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