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- PDB-4k68: Structure of a novel GH10 endoxylanase retrieved from sugarcane s... -

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Basic information

Entry
Database: PDB / ID: 4k68
TitleStructure of a novel GH10 endoxylanase retrieved from sugarcane soil metagenome
ComponentsGH10 xylanase
KeywordsHYDROLASE / GH10 / xylanase
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSantos, C.R. / Polo, C.C. / Alvarez, T.M. / Paixao, D.A.A. / Almeida, R.F. / Pereira, I.O. / Squina, F.M. / Murakami, M.T.
CitationJournal: Plos One / Year: 2013
Title: Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome.
Authors: Alvarez, T.M. / Goldbeck, R. / dos Santos, C.R. / Paixao, D.A. / Goncalves, T.A. / Franco Cairo, J.P. / Almeida, R.F. / de Oliveira Pereira, I. / Jackson, G. / Cota, J. / Buchli, F. / ...Authors: Alvarez, T.M. / Goldbeck, R. / dos Santos, C.R. / Paixao, D.A. / Goncalves, T.A. / Franco Cairo, J.P. / Almeida, R.F. / de Oliveira Pereira, I. / Jackson, G. / Cota, J. / Buchli, F. / Citadini, A.P. / Ruller, R. / Polo, C.C. / de Oliveira Neto, M. / Murakami, M.T. / Squina, F.M.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH10 xylanase
B: GH10 xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2263
Polymers87,1342
Non-polymers921
Water2,882160
1
A: GH10 xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6592
Polymers43,5671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH10 xylanase


Theoretical massNumber of molelcules
Total (without water)43,5671
Polymers43,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.877, 116.442, 82.811
Angle α, β, γ (deg.)90.00, 99.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GH10 xylanase


Mass: 43566.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: double-crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.74→41.2 Å / Num. obs: 20118 / % possible obs: 97.57 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.143
Reflection shellResolution: 2.74→2.85 Å / Rmerge(I) obs: 0.468 / % possible all: 87.2

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Processing

Software
NameVersionClassification
NatXraydata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→41.2 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1025 5.1 %RANDOM
Rwork0.2036 ---
obs0.2062 20087 97.43 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.241 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.923 Å2-0 Å2-8.9128 Å2
2--1.0298 Å2-0 Å2
3----8.9528 Å2
Refinement stepCycle: LAST / Resolution: 2.74→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 6 160 5736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025732
X-RAY DIFFRACTIONf_angle_d0.5887755
X-RAY DIFFRACTIONf_dihedral_angle_d11.8682152
X-RAY DIFFRACTIONf_chiral_restr0.043818
X-RAY DIFFRACTIONf_plane_restr0.003993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.88450.33221290.2792435X-RAY DIFFRACTION87
2.8845-3.06520.33591430.26252674X-RAY DIFFRACTION96
3.0652-3.30170.26921640.23562758X-RAY DIFFRACTION99
3.3017-3.63380.27651270.2072798X-RAY DIFFRACTION100
3.6338-4.15920.21531500.17712797X-RAY DIFFRACTION100
4.1592-5.23850.21491600.15972778X-RAY DIFFRACTION100
5.2385-41.20.25421520.2032822X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.11191.0882.07773.04590.86822.432-0.37670.31040.3109-0.39070.25430.3629-0.4566-0.02680.17790.4326-0.0197-0.01710.1770.07810.2052-17.24594.659784.4618
22.56952.4844-0.19884.26380.64790.74830.13280.15770.15040.5441-0.36750.2972-0.3897-0.1251-0.15960.3826-0.0631-0.19910.2635-0.01210.2353-26.601-12.207584.0318
31.49380.77391.27881.96771.05672.61860.00280.1637-0.1774-0.00760.0891-0.12210.1190.1703-0.08280.1744-0.0004-0.03290.10540.01560.1083-13.6493-15.063988.2148
45.5725-1.7017-1.11363.60120.99362.7552-0.09-0.5301-0.01220.25030.12940.0809-0.12450.03-0.06310.3385-0.0015-0.11870.20080.01960.1755-11.93153.7933103.6792
51.7002-0.31540.51731.18730.18581.5406-0.0241-0.01510.1223-0.0822-0.0398-0.0632-0.0505-0.14440.05950.28650.0118-0.05220.0905-0.01930.1305-2.6777-22.8598137.1227
61.7112-0.0431-1.97940.4120.89986.9075-0.4264-0.0895-0.52790.3063-0.1825-0.06730.61470.99750.53530.50210.1165-0.10910.33690.06260.4914-0.7869-32.0229117.452
72.44240.8006-1.51631.8682-1.21355.23040.0587-0.05280.0289-0.0355-0.0120.07620.1278-0.2338-0.04750.32830.0404-0.12680.155-0.01780.2011-12.36-25.9992118.5878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 32:106)
2X-RAY DIFFRACTION2chain 'A' and (resseq 107:135)
3X-RAY DIFFRACTION3chain 'A' and (resseq 136:275)
4X-RAY DIFFRACTION4chain 'A' and (resseq 276:379)
5X-RAY DIFFRACTION5chain 'B' and (resseq 34:263)
6X-RAY DIFFRACTION6chain 'B' and (resseq 264:306)
7X-RAY DIFFRACTION7chain 'B' and (resseq 307:378)

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