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- PDB-1h14: Structure of a cold-adapted family 8 xylanase -

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Basic information

Entry
Database: PDB / ID: 1h14
TitleStructure of a cold-adapted family 8 xylanase
ComponentsENDO-1,4-BETA-XYLANASEXylanase
KeywordsHYDROLASE / XYLAN DEGRADATION / PSYCHROPHILIC / COLD ADAPTATION / TEMPERATURE / GLYCOSYL HYDROLASE / FAMILY 8
Function / homology
Function and homology information


cellulase / cellulase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 8 / Glycoside hydrolase, family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPSEUDOALTEROMONAS HALOPLANKTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)46,0241
Polymers46,0241
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.087, 90.891, 98.023
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 / Xylanase


Mass: 46023.781 Da / Num. of mol.: 1 / Mutation: YES
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION FROM ASP 165 ASN

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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 IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE. SUCCESS RATE 1/20
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: 1.5→20 Å / Num. obs: 74080 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.21
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.57 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. measured all: 479600
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 95.3 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE

Resolution: 1.5→65.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.419 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3721 5 %RANDOM
Rwork0.143 ---
obs0.145 70042 99.7 %-
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: 9.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 356 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0213378
X-RAY DIFFRACTIONr_bond_other_d0.0020.022781
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9064633
X-RAY DIFFRACTIONr_angle_other_deg3.68936523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6883426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17415535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1530.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023920
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02749
X-RAY DIFFRACTIONr_nbd_refined0.2390.3710
X-RAY DIFFRACTIONr_nbd_other0.1990.32688
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.3810.522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8280.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1741.52039
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97223282
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94331339
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.274.51341
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 273
Rwork0.195 4997
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.1707 / Rfactor Rwork: 0.1433
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.029
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.169

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