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- PDB-3m81: Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTO... -

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Basic information

Entry
Database: PDB / ID: 3m81
TitleCrystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.50 A resolution (native apo structure)
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / AXE1
Function / homology
Function and homology information


xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / cytoplasm
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
ACETATE ION / Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2012
Title: Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.
Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / ...Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / Deacon, A.M. / van der Oost, J. / Lesley, S.A. / Elsliger, M.A. / Kengen, S.W. / Wilson, I.A.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.7Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,12230
Polymers231,9786
Non-polymers1,14524
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21880 Å2
ΔGint-220 kcal/mol
Surface area63270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.460, 103.790, 221.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 3 - 323 / Label seq-ID: 15 - 335

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Acetyl xylan esterase


Mass: 38662.922 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0077, TM_0077 / Plasmid: MH1 / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WXT2

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Non-polymers , 5 types, 531 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.5→48.795 Å / Num. obs: 83045 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.247 Å2 / Rmerge(I) obs: 0.207 / Net I/σ(I): 14.37
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.560.0112.99071860821100
2.56-2.640.0113.28805859111100
2.64-2.710.0113.88636657941100
2.71-2.80.0114.68286355561100
2.8-2.890.0115.48116554551100
2.89-2.990.0116.47804952401100
2.99-3.10.01187507850431100
3.1-3.230.0119.47287449031100
3.23-3.370.01112.77001347191100
3.37-3.540.01114.56642644881100
3.54-3.730.01119.36339643071100
3.73-3.950.01123.55961740561100
3.95-4.230.01126.65564138081100
4.23-4.560.01129.45206135751100
4.56-50.011314788033151100
5-5.590.01127.34277829861100
5.59-6.450.01125.73769626961100
6.45-7.910.01130.93228922671100
7.91-11.180.01143.72542218031100
11.18-48.7950.01145.8136261041198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
PHASERphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: 1vlq

1vlq


Resolution: 2.5→48.795 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.194 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.454 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CALCIUM (CA), CHLORIDE (CL) AND ACETATE (ACT) IONS FROM CRYSTALLIZATION CONDITIONS, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4200 5.1 %RANDOM
Rwork0.167 ---
obs0.169 83045 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.04 Å2 / Biso mean: 29.065 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15568 0 54 507 16129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02216135
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211301
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.95721874
X-RAY DIFFRACTIONr_angle_other_deg0.972327234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95451937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49623.03792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.952152544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77215114
X-RAY DIFFRACTIONr_chiral_restr0.0880.22225
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218125
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023659
X-RAY DIFFRACTIONr_nbd_refined0.2180.23262
X-RAY DIFFRACTIONr_nbd_other0.1970.211698
X-RAY DIFFRACTIONr_nbtor_refined0.1930.27855
X-RAY DIFFRACTIONr_nbtor_other0.0880.28140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2595
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.27
X-RAY DIFFRACTIONr_mcbond_it1.748310023
X-RAY DIFFRACTIONr_mcbond_other0.21733892
X-RAY DIFFRACTIONr_mcangle_it2.577515576
X-RAY DIFFRACTIONr_scbond_it4.69887249
X-RAY DIFFRACTIONr_scangle_it5.97116298
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1853TIGHT POSITIONAL0.050.05
2B1853TIGHT POSITIONAL0.050.05
3C1853TIGHT POSITIONAL0.050.05
4D1853TIGHT POSITIONAL0.040.05
5E1853TIGHT POSITIONAL0.050.05
6F1853TIGHT POSITIONAL0.040.05
1A2550MEDIUM POSITIONAL0.280.5
2B2550MEDIUM POSITIONAL0.280.5
3C2550MEDIUM POSITIONAL0.290.5
4D2550MEDIUM POSITIONAL0.250.5
5E2550MEDIUM POSITIONAL0.290.5
6F2550MEDIUM POSITIONAL0.230.5
1A1853TIGHT THERMAL0.150.5
2B1853TIGHT THERMAL0.170.5
3C1853TIGHT THERMAL0.140.5
4D1853TIGHT THERMAL0.150.5
5E1853TIGHT THERMAL0.180.5
6F1853TIGHT THERMAL0.170.5
1A2550MEDIUM THERMAL1.012
2B2550MEDIUM THERMAL1.082
3C2550MEDIUM THERMAL0.942
4D2550MEDIUM THERMAL1.082
5E2550MEDIUM THERMAL1.152
6F2550MEDIUM THERMAL1.152
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 317 -
Rwork0.258 5751 -
all-6068 -
obs--99.9 %

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