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- PDB-6fj4: Structure of FAE solved by SAD from data collected at the peak of... -

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Basic information

Entry
Database: PDB / ID: 6fj4
TitleStructure of FAE solved by SAD from data collected at the peak of the Selenium absorption edge on ID30B
ComponentsEndo-1,4-beta-xylanase Y
KeywordsHYDROLASE
Function / homology
Function and homology information


cellulosome / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Clostridium cellulosome enzymes repeated domain signature. / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / Alpha/Beta hydrolase fold, catalytic domain / EF-hand calcium-binding domain. / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Endo-1,4-beta-xylanase Y
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMcCarthy, A.A. / Mueller-Dieckmann, C.
CitationJournal: J Synchrotron Radiat / Year: 2018
Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.
Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation_author / pdbx_related_exp_data_set
Item: _citation_author.identifier_ORCID / _pdbx_related_exp_data_set.data_reference
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_conn_type.id

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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 Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5999
Polymers32,7571
Non-polymers8428
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-34 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.023, 112.023, 65.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Endo-1,4-beta-xylanase Y / Xylanase Y / 1 / 4-beta-D-xylan xylanohydrolase Y / XylY


Mass: 32757.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: xynY / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P51584, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 50 mM CdSO4, 5% (v/v) glycerol, and 1 M Na-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2017
Details: Be CRL (vertical) and Rh Elliptical mirror (horizontal)
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→79.21 Å / Num. obs: 46013 / % possible obs: 96.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Rrim(I) all: 0.091 / Net I/σ(I): 11.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2462 / CC1/2: 0.318 / Rpim(I) all: 0.84 / Rrim(I) all: 1.83 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→79.21 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.498 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17786 2487 5.4 %RANDOM
Rwork0.16024 ---
obs0.16118 43496 98.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0 Å2
2--0.37 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.7→79.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 22 194 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192440
X-RAY DIFFRACTIONr_bond_other_d0.0020.022040
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.943292
X-RAY DIFFRACTIONr_angle_other_deg1.02634749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8923.858127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.183159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
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_it1.0351.9051141
X-RAY DIFFRACTIONr_mcbond_other1.0341.9051140
X-RAY DIFFRACTIONr_mcangle_it1.6192.8511427
X-RAY DIFFRACTIONr_mcangle_other1.6192.8511428
X-RAY DIFFRACTIONr_scbond_it2.0672.161291
X-RAY DIFFRACTIONr_scbond_other1.9172.1451287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.513.121855
X-RAY DIFFRACTIONr_long_range_B_refined5.20923.0712657
X-RAY DIFFRACTIONr_long_range_B_other5.1622.5992622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 192 -
Rwork0.368 3195 -
obs--99.71 %

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