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- PDB-3wp4: The crystal structure of native CDBFV from Neocallimastix patriciarum -

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Basic information

Entry
Database: PDB / ID: 3wp4
TitleThe crystal structure of native CDBFV 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: 1.27 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDBFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8602
Polymers24,7641
Non-polymers961
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.770, 92.770, 42.900
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: 24764.111 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) / Strain (production host): X33 / References: UniProt: Q9UV68*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 2M ammonium sulfate, 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: 1.27→25 Å / Num. obs: 55625 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 49.4
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 7.9 / Num. unique all: 5510 / % possible all: 99.9

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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: 1IGO

1igo


Resolution: 1.27→24.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.043 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16603 2825 5.1 %RANDOM
Rwork0.13925 ---
obs0.14058 52832 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.11 Å20 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.27→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 5 332 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191798
X-RAY DIFFRACTIONr_bond_other_d0.0010.021575
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9212437
X-RAY DIFFRACTIONr_angle_other_deg0.7743.0023624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46624.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19115267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.575156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
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_restr5.12633373
X-RAY DIFFRACTIONr_sphericity_free25.3655100
X-RAY DIFFRACTIONr_sphericity_bonded6.51253559
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 210 -
Rwork0.147 3886 -
obs--99.56 %
Refinement TLS params.Method: refined / Origin x: 26.9688 Å / Origin y: -16.6904 Å / Origin z: -5.4136 Å
111213212223313233
T0.0112 Å2-0.01 Å20.0001 Å2-0.0218 Å20.0034 Å2--0.0052 Å2
L0.5398 °20.1576 °20.063 °2-0.6814 °2-0.0884 °2--0.391 °2
S-0.0239 Å °0.0476 Å °-0.0242 Å °-0.0079 Å °0.0322 Å °-0.031 Å °-0.022 Å °0.0174 Å °-0.0083 Å °

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