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- PDB-4h35: Feruloyl Esterase Domain of XYNY from Clostridium thermocellum be... -

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Basic information

Entry
Database: PDB / ID: 4h35
TitleFeruloyl Esterase Domain of XYNY from Clostridium thermocellum before exposure to 266nm UV laser
ComponentsEndo-1,4-beta-xylanase Y
KeywordsHYDROLASE / Alpha and beta proteins
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 / UV-RIP / 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. / Royant, A. / Panjikar, S. / de Sanctis, D.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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)69,43210
Polymers68,5332
Non-polymers8998
Water5,675315
1
A: 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
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

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Components

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


Mass: 34266.562 Da / Num. of mol.: 2 / Fragment: feruloyl esterase domain (UNP residues 792-1077)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: xynY / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 1 M sodium acetate, 50 mM cadmium acetate, 5% glycerol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 15, 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. all: 63630 / Num. obs: 63630 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.115 / Net I/σ(I): 13.76

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Processing

Software
NameVersionClassification
CrysalisProdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: UV-RIP / Resolution: 1.9→14.86 Å / SU ML: 0.15 / σ(F): 1.01 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 3257 5.11 %RANDOM
Rwork0.1574 ---
obs0.1585 63616 99.67 %-
all-63616 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 8 315 4903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084754
X-RAY DIFFRACTIONf_angle_d1.1076476
X-RAY DIFFRACTIONf_dihedral_angle_d13.2661672
X-RAY DIFFRACTIONf_chiral_restr0.08640
X-RAY DIFFRACTIONf_plane_restr0.005850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92150.22362110.22113754X-RAY DIFFRACTION96
1.9215-1.94410.23741990.23819X-RAY DIFFRACTION100
1.9441-1.96770.23382060.19173837X-RAY DIFFRACTION100
1.9677-1.99260.19852000.18223867X-RAY DIFFRACTION100
1.9926-2.01870.19422100.18413849X-RAY DIFFRACTION100
2.0187-2.04630.24082160.18323858X-RAY DIFFRACTION100
2.0463-2.07550.21652050.18733815X-RAY DIFFRACTION100
2.0755-2.10640.20371970.16383880X-RAY DIFFRACTION100
2.1064-2.13920.18292290.15983798X-RAY DIFFRACTION100
2.1392-2.17420.17092170.15683909X-RAY DIFFRACTION100
2.1742-2.21150.18321890.15353818X-RAY DIFFRACTION100
2.2115-2.25160.1971930.15113862X-RAY DIFFRACTION100
2.2516-2.29480.16691850.14993862X-RAY DIFFRACTION100
2.2948-2.34140.16431880.15583852X-RAY DIFFRACTION100
2.3414-2.39210.15812430.14553824X-RAY DIFFRACTION100
2.3921-2.44750.17272170.14483837X-RAY DIFFRACTION100
2.4475-2.50850.15982010.14923886X-RAY DIFFRACTION100
2.5085-2.5760.18112020.15093847X-RAY DIFFRACTION100
2.576-2.65130.17922380.15553818X-RAY DIFFRACTION100
2.6513-2.73640.18952090.15493844X-RAY DIFFRACTION100
2.7364-2.83360.17682300.15943866X-RAY DIFFRACTION100
2.8336-2.94620.18422370.1633822X-RAY DIFFRACTION100
2.9462-3.07910.16261900.15773859X-RAY DIFFRACTION100
3.0791-3.23990.18212100.15943839X-RAY DIFFRACTION100
3.2399-3.44050.17082070.16123862X-RAY DIFFRACTION100
3.4405-3.70240.18041770.14893865X-RAY DIFFRACTION100
3.7024-4.0680.14462270.13673846X-RAY DIFFRACTION100
4.068-4.64090.141990.12423837X-RAY DIFFRACTION99
4.6409-5.7890.12821780.14063843X-RAY DIFFRACTION99
5.789-14.86090.19322030.16873803X-RAY DIFFRACTION99

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