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- PDB-4bag: Feruloyl Esterase Domain of XYNY from Clostridium thermocellum af... -

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Basic information

Entry
Database: PDB / ID: 4bag
TitleFeruloyl Esterase Domain of XYNY from Clostridium thermocellum after exposure to 266nm UV laser
ComponentsENDO-1,4-BETA-XYLANASE Y
KeywordsHYDROLASE
Function / homology
Function and homology information


cellulosome / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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 / OTHER / Resolution: 1.9 Å
AuthorsPereira, P.J.B. / de Sanctis, D.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: In-House Uv Radiation-Damage-Induced Phasing of Selenomethionine-Labeled Protein Structures.
Authors: Pereira, P.J.B. / Royant, A. / Panjikar, S. / De Sanctis, D.
History
DepositionSep 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.type
Revision 2.1Jun 6, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _software.version
Revision 2.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52511
Polymers68,5332
Non-polymers9919
Water5,729318
1
A: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8086
Polymers34,2671
Non-polymers5425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,4-BETA-XYLANASE Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7165
Polymers34,2671
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.370, 108.400, 112.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, 0.01354, 0.002644), (0.004003, 0.1014, 0.9948), (0.01321, 0.9948, -0.1014)
Vector: 14.5997, 70.6779, -78.5817)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE Y / XYLANASE Y / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE Y / XYLY


Mass: 34266.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51584, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.9 Å3/Da / Density % sol: 58.8 % / Description: NONE
Crystal growpH: 7.4
Details: HEPES PH 7.5 100MM, NA ACETATE 1M, CD ACETATE 50 MM, GLYCEROL 5%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION GEMINI / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: AGILENT / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 63630 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 10.13 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 99.3

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→14.86 Å / SU ML: 0.13 / σ(F): 1.08 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 6191 5.1 %
Rwork0.1671 --
obs0.1682 63588 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 14 318 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084768
X-RAY DIFFRACTIONf_angle_d1.1136495
X-RAY DIFFRACTIONf_dihedral_angle_d13.2481678
X-RAY DIFFRACTIONf_chiral_restr0.082641
X-RAY DIFFRACTIONf_plane_restr0.005853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92150.27161800.24423658X-RAY DIFFRACTION93
1.9215-1.94410.26921970.22533819X-RAY DIFFRACTION100
1.9441-1.96770.22751890.2133839X-RAY DIFFRACTION99
1.9677-1.99260.23751890.20583866X-RAY DIFFRACTION99
1.9926-2.01870.23092160.2013839X-RAY DIFFRACTION100
2.0187-2.04630.22342100.19833864X-RAY DIFFRACTION100
2.0463-2.07550.20771770.19593837X-RAY DIFFRACTION100
2.0755-2.10640.21331990.17783865X-RAY DIFFRACTION99
2.1064-2.13920.22671900.17743833X-RAY DIFFRACTION100
2.1392-2.17420.22951860.17193931X-RAY DIFFRACTION100
2.1742-2.21150.22871920.16833812X-RAY DIFFRACTION100
2.2115-2.25160.20522220.16253828X-RAY DIFFRACTION100
2.2516-2.29480.17292050.16023844X-RAY DIFFRACTION100
2.2948-2.34140.20092010.16283843X-RAY DIFFRACTION100
2.3414-2.39210.20052210.14773850X-RAY DIFFRACTION100
2.3921-2.44750.16481970.15113855X-RAY DIFFRACTION100
2.4475-2.50850.16812180.15293869X-RAY DIFFRACTION100
2.5085-2.5760.15852390.15463812X-RAY DIFFRACTION100
2.576-2.65130.18442240.16113832X-RAY DIFFRACTION100
2.6513-2.73640.17991950.16393855X-RAY DIFFRACTION100
2.7364-2.83360.21112270.16723870X-RAY DIFFRACTION100
2.8336-2.94620.19762140.16723842X-RAY DIFFRACTION100
2.9462-3.07910.18582250.16383824X-RAY DIFFRACTION100
3.0791-3.23990.1852030.16773845X-RAY DIFFRACTION100
3.2399-3.44050.18642200.16683849X-RAY DIFFRACTION100
3.4405-3.70240.1622200.15653823X-RAY DIFFRACTION100
3.7024-4.0680.15481720.13963890X-RAY DIFFRACTION100
4.068-4.64090.12422380.13313778X-RAY DIFFRACTION99
4.6409-5.7890.14061980.15253785X-RAY DIFFRACTION98
5.789-14.86090.2082270.17073746X-RAY DIFFRACTION98

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