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- PDB-1axk: ENGINEERED BACILLUS BIFUNCTIONAL ENZYME GLUXYN-1 -

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Basic information

Entry
Database: PDB / ID: 1axk
TitleENGINEERED BACILLUS BIFUNCTIONAL ENZYME GLUXYN-1
ComponentsGLUXYN-1
KeywordsFUSION PROTEIN / GLUXYN-1 / BIFUNCTIONAL / 1 / 4-BETA-XYLANASE / 3-1 / 4-BETA-GLUCANASE / HYBRID ENZYME
Function / homology
Function and homology information


licheninase / licheninase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain ...Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A / Beta-glucanase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAy, J. / Heinemann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain.
Authors: Ay, J. / Gotz, F. / Borriss, R. / Heinemann, U.
History
DepositionOct 16, 1997Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_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_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUXYN-1
B: GLUXYN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7064
Polymers87,6252
Non-polymers802
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.270, 133.700, 77.950
Angle α, β, γ (deg.)90.00, 99.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.993795, 0.034209, 0.105835), (0.111119, -0.347062, -0.931236), (0.004875, 0.937218, -0.34871)-5.7263, 22.7062, -58.4025
2given(0.999869, 0.008888, -0.013542), (-0.006408, -0.550771, -0.834632), (-0.014877, 0.834609, -0.550642)-3.582, 31.9424, -53.3662
3given(0.993795, 0.034209, 0.105835), (0.111119, -0.347062, -0.931236), (0.004875, 0.937218, -0.34871)-5.7263, 22.7062, -58.4025

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Components

#1: Protein GLUXYN-1


Mass: 43812.676 Da / Num. of mol.: 2
Fragment: FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: ACTIVE AS BOTH A 1,3-1,4-BETA-GLUCANASE AND A 1,4-BETA-XYLANASE
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: DH5-ALPHA / Fragment: 1,4-BETA-XYLANASE DOMAIN / Plasmid: PFD1 / Cell line (production host): DH5-ALPHA / Production host: Escherichia coli (E. coli)
References: UniProt: P23904, UniProt: P18429, licheninase, endo-1,4-beta-xylanase
#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


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 46.4 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 8.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.8 mg/mlprotein1drop
220 mMTris-HCl1drop
32 mM1dropCaCl2
440 mMKP1reservoir
516 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 48499 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.98 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.23 / % possible all: 80
Reflection
*PLUS
Num. measured all: 165157
Reflection shell
*PLUS
Lowest resolution: 2.17 Å / % possible obs: 80 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CIRCULARLY PERMUTED 1,3-1,4-ENDO-BETA-GLUCANASE CPMAC57 (PDB ENTRY 1CPN) AND BACILLUS CIRCULANS 1,3-ENDO-BETA-XYLANASE (PDB ENTRY 1BCX).

1cpn

1bcx


Resolution: 2.1→19.96 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2440 5 %RANDOM
Rwork0.176 ---
obs0.177 48499 91.3 %-
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å23.806 Å2
2--2.168 Å20 Å2
3---0.464 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 2 312 6533
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5842
X-RAY DIFFRACTIONp_mcangle_it2.3493
X-RAY DIFFRACTIONp_scbond_it1.6652
X-RAY DIFFRACTIONp_scangle_it2.4553
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1330.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.67
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor015

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