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- PDB-1w2v: The 3-dimensional structure of a thermostable mutant of a xylanas... -

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Basic information

Entry
Database: PDB / ID: 1w2v
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 / endo-1,4-beta-xylanase activity / 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: 1.55 Å
AuthorsAndrews, S. / Taylor, E.J. / Pell, G.N. / Vincent, F. / Ducros, V.M.A. / Davies, G.J. / Lakey, J.H. / Glbert, 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 9, 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 1.3Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_strain / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.4Dec 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_unobs_or_zero_occ_atoms / 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 / _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 1.5Oct 16, 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" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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)77,4145
Polymers77,2712
Non-polymers1423
Water12,809711
1
A: ENDO-1,4-BETA-XYLANASE A PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6762
Polymers38,6361
Non-polymers401
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)38,7383
Polymers38,6361
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.609, 95.609, 150.315
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: (0.99764, -0.04997, 0.04716), (0.05578, 0.18822, -0.98054), (0.04012, 0.98086, 0.19056)
Vector: 7.53551, 68.68463, -30.90608)

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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: 38635.727 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
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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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 IN CHAIN A AND B, ALA 344 THR AND ASP 526 GLU
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: 44.5 %

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorDate: Jan 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 100882 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.96
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 10.07 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLX

1clx


Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.947 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 5034 5 %RANDOM
Rwork0.149 ---
obs0.151 95756 100 %-
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: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 6 711 6129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217897
X-RAY DIFFRACTIONr_bond_other_d0.0010.026681
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.90610847
X-RAY DIFFRACTIONr_angle_other_deg0.774315600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61851042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98624.41424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.529151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.741559
X-RAY DIFFRACTIONr_chiral_restr0.0920.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029501
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021708
X-RAY DIFFRACTIONr_nbd_refined0.250.21442
X-RAY DIFFRACTIONr_nbd_other0.2350.25867
X-RAY DIFFRACTIONr_nbtor_refined0.1930.23100
X-RAY DIFFRACTIONr_nbtor_other0.0960.23524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.2546
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2181.55067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64828003
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41533247
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2684.52841
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: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.185 375
Rwork0.115 6967

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