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- PDB-1w32: The 3-dimensional structure of a thermostable mutant of a xylanas... -

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Basic information

Entry
Database: PDB / ID: 1w32
TitleThe 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus
ComponentsENDO-1,4-BETA-XYLANASE A PRECURSOR
KeywordsHYDROLASE / XYLANASE / MUTANT / CALCIUM ION / THERMOSTABLE / GLYCOSYLE HYDROLASE / FAMILY 10 / ERROR PRONE PCR
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAndrews, S. / Taylor, E.J. / Pell, G.N. / Vincent, F. / Ducros, V.M.A. / Davies, G.J. / Lakey, J.H. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Use of Forced Protein Evolution to Investigate and Improve Stability of Family 10 Xylanases: The Production of Ca2+-Independent Stable Xylanases
Authors: Andrews, S. / Taylor, E.J. / Pell, G.N. / Vincent, F. / Ducros, V.M.A. / Davies, G.J. / Lakey, J.H. / Gilbert, H.J.
History
DepositionJul 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE A PRECURSOR
B: ENDO-1,4-BETA-XYLANASE A PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,82013
Polymers77,1812
Non-polymers63911
Water18,5191028
1
A: ENDO-1,4-BETA-XYLANASE A PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7554
Polymers38,5911
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO-1,4-BETA-XYLANASE A PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0659
Polymers38,5911
Non-polymers4758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.343, 95.343, 150.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997, -0.056, 0.05), (0.06, 0.183, -0.981), (0.045, 0.982, 0.186)
Vector: 7.74292, 68.86922, -30.29871)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE A PRECURSOR / XYLANASE A / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE A / XYLA


Mass: 38590.691 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 265-611 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria)
Description: ORGANISM FORMERLY KNOWN AS PSEUDOMONAS FLUORESCENS
Plasmid: PET-16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GM83 DE3 / References: UniProt: P14768, 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. ENGINEERED MUTATION: ...CATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. ENGINEERED MUTATION: ASN 526 ASP IN CHAINS A, B
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: 2.2 Å3/Da / Density % sol: 44 %

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorDate: Dec 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 213551 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.55 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.07
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.42 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLX

1clx


Resolution: 1.2→81.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.144 10712 5 %RANDOM
Rwork0.121 ---
obs0.122 202740 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 38 1028 6472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217354
X-RAY DIFFRACTIONr_bond_other_d00.026187
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.91610096
X-RAY DIFFRACTIONr_angle_other_deg0.763314442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83124.375400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.076151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4741555
X-RAY DIFFRACTIONr_chiral_restr0.0840.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028892
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021607
X-RAY DIFFRACTIONr_nbd_refined0.2480.21429
X-RAY DIFFRACTIONr_nbd_other0.2310.25839
X-RAY DIFFRACTIONr_nbtor_refined0.1930.23168
X-RAY DIFFRACTIONr_nbtor_other0.0940.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2756
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.293
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.54690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46727422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1233052
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8414.52673
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 743
Rwork0.172 14217

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