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- PDB-3wp5: The crystal structure of mutant CDBFV E109A from Neocallimastix p... -

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Basic information

Entry
Database: PDB / ID: 3wp5
TitleThe crystal structure of mutant CDBFV E109A from Neocallimastix patriciarum
ComponentsCDBFV
KeywordsHYDROLASE / xylanase / regulatory N-terminal region / disulfide bond / industrial enzyme / beta-jellyroll fold
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 ...CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesNeocallimastix patriciarum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsCheng, Y.S. / Chen, C.C. / Huang, C.H. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural analysis of a glycoside hydrolase family 11 xylanase from Neocallimastix patriciarum: insights into the molecular basis of a thermophilic enzyme.
Authors: Cheng, Y.S. / Chen, C.C. / Huang, C.H. / Ko, T.P. / Luo, W. / Huang, J.W. / Liu, J.R. / Guo, R.T.
History
DepositionJan 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDBFV


Theoretical massNumber of molelcules
Total (without water)24,6351
Polymers24,6351
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.857, 92.857, 43.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein CDBFV / xylanase


Mass: 24634.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neocallimastix patriciarum (fungus) / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9UV68*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS PROTEIN HAS MUTATION E109A

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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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate, pH 6.5, 0.2M ammonium sulfate, 26% PEG 8000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→25 Å / Num. obs: 50174 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 44.8
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5000 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WP4

3wp4


Resolution: 1.32→24.86 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.434 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18263 2544 5.1 %RANDOM
Rwork0.14673 ---
obs0.14851 47540 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.05 Å20 Å2
2--0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.32→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 351 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9172419
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49824.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48215265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.805156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211403
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.65631785
X-RAY DIFFRACTIONr_sphericity_free30.023596
X-RAY DIFFRACTIONr_sphericity_bonded7.68851993
LS refinement shellResolution: 1.318→1.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 181 -
Rwork0.212 3465 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: -0.8588 Å / Origin y: -32.048 Å / Origin z: -4.8069 Å
111213212223313233
T0.012 Å20.0107 Å2-0.0066 Å2-0.0141 Å2-0.0028 Å2--0.0137 Å2
L0.596 °2-0.019 °2-0.144 °2-0.36 °2-0.1604 °2--0.2332 °2
S0.0451 Å °0.0304 Å °-0.0229 Å °-0.0277 Å °-0.0553 Å °-0.0058 Å °0.001 Å °0.0302 Å °0.0102 Å °

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