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- PDB-1h12: Structure of a cold-adapted family 8 xylanase -

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Basic information

Entry
Database: PDB / ID: 1h12
TitleStructure of a cold-adapted family 8 xylanase
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLAN DEGRADATION / PSYCHROPHILIC / COLD ADAPTATION / TEMPERATURE / GLYCOSYL HYDROLASE / FAMILY 8
Function / homology
Function and homology information


cellulase / cellulase activity / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
beta-D-xylopyranose / alpha-D-xylopyranose / cellulase
Similarity search - Component
Biological speciesPSEUDOALTEROMONAS HALOPLANKTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVan Petegem, F. / Collins, T. / Meuwis, M.A. / Feller, G. / Gerday, C. / Van Beeumen, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Structure of a Cold-Adapted Family 8 Xylanase at 1.3 A Resolution: Structural Adaptations to Cold and Investigation of the Active Site
Authors: Van Petegem, F. / Collins, T. / Meuwis, M.A. / Gerday, C. / Feller, G. / Van Beeumen, J.
History
DepositionJul 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: 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: ENDO-1,4-BETA-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3253
Polymers46,0251
Non-polymers3002
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.972, 90.734, 97.581
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 ENDO-1,4-BETA-XYLANASE


Mass: 46024.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOALTEROMONAS HALOPLANKTIS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8RJN8, endo-1,4-beta-xylanase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.43 Å3/Da / Density % sol: 47.5 %
Description: CRYO-ANNEALING LOWERS THE MOSAICITY AND INCREASES THE RESOLUTION LIMIT
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS, 50MM NACL, 2% TREHALOSE, PH 7.5. ADD EQUAL VOLUME OF 70% MPD, 0.1M PHOSPHATE BUFFER PH 7.0 WITH 10MG/ML XYLOBIOSE IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE.
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Details: Van Petegem, F., (2002) Acta Crystallogr., D58, 1494.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlprotein1drop
270 %MPD1reservoir
30.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 141707 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 43.52
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.69 / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Num. measured all: 1757738
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 91.9 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE WITHOUT LIGAND

Resolution: 1.2→65.94 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.752 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13 7056 5 %RANDOM
Rwork0.107 ---
obs0.108 133682 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 20 390 3613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0213367
X-RAY DIFFRACTIONr_bond_other_d0.0020.022781
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9134609
X-RAY DIFFRACTIONr_angle_other_deg3.48336513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8663420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1960.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023878
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02742
X-RAY DIFFRACTIONr_nbd_refined0.2440.3700
X-RAY DIFFRACTIONr_nbd_other0.1970.32654
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.3710.524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6841.52031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44123259
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.88231336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6134.51341
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
Rfree0.199 482
Rwork0.186 9160
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.1302 / Rfactor Rwork: 0.107
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.586

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