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- PDB-2uwf: Crystal structure of family 10 xylanase from Bacillus halodurans -

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Basic information

Entry
Database: PDB / ID: 2uwf
TitleCrystal structure of family 10 xylanase from Bacillus halodurans
ComponentsALKALINE ACTIVE ENDOXYLANASE
KeywordsHYDROLASE / XYLAN DEGRADATION / XYLANASE STRUCTURE / GLYCOSIDASE / ALKALIPHILIC / ENDOXYLANASE / BACILLUS HALODURANS / ALKALINE ADAPTATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region / metal ion binding
Similarity search - Function
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Endo-1,4-beta-xylanase A / Beta-xylanase
Similarity search - Component
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMamo, G. / Thunnissen, M. / Hatti-Kaul, R. / Mattiasson, B.
CitationJournal: Biochimie / Year: 2009
Title: An Alkaline Active Xylanase: Insights Into Mechanisms of High Ph Catalytic Adaptation
Authors: Mamo, G. / Thunnissen, M. / Hatti-Kaul, R. / Mattiasson, B.
History
DepositionMar 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALKALINE ACTIVE ENDOXYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9466
Polymers41,7221
Non-polymers2245
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.602, 53.586, 127.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALKALINE ACTIVE ENDOXYLANASE / ENDOXYLANASE


Mass: 41721.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 47-396
Source method: isolated from a genetically manipulated source
Details: ADDITIONAL HIS-TAG PRESENT IN THIS ENTRY. I359D360H361H362H363H364H365H366
Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Strain: S7 / Plasmid: PET22 BPLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q17TM8, UniProt: P07528*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: NONE
Crystal growDetails: 30 % (V/V) 2-METHYL-2, 4-PENTANEDIOL, 20 MM CACL2 AND 100 MM SODIUM ACETATE BUFFER (PH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9707
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 22, 2004 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9707 Å / Relative weight: 1
ReflectionResolution: 2.1→65 Å / Num. obs: 21002 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HIZ

1hiz


Resolution: 2.1→64.55 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.465 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1067 5.1 %RANDOM
Rwork0.185 ---
obs0.188 19843 97.8 %-
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: 21.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 5 210 3168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213038
X-RAY DIFFRACTIONr_bond_other_d0.0010.022021
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9154132
X-RAY DIFFRACTIONr_angle_other_deg0.92334888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34124.607178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39115489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3691518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_nbd_refined0.2220.2725
X-RAY DIFFRACTIONr_nbd_other0.2030.22211
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21493
X-RAY DIFFRACTIONr_nbtor_other0.0890.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.51839
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40422864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17131427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4034.51268
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 81
Rwork0.194 1486

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