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- PDB-7nn3: A carbohydrate esterase family 15 (CE15) glucuronoyl esterase fro... -

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Basic information

Entry
Database: PDB / ID: 7nn3
TitleA carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Caldicellulosiruptor kristjansonii
ComponentsBeta-xylanase
KeywordsHYDROLASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / polysaccharide catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Glucuronyl esterase, fungi / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain ...Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Glucuronyl esterase, fungi / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / 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 / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta-xylanase
Similarity search - Component
Biological speciesCaldicellulosiruptor kristjanssonii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88948348333 Å
AuthorsKrska, D. / Mazurkewich, S. / Navarro Poulsen, J. / Larsbrink, J. / Lo Leggio, L.
Funding support Sweden, Denmark, 4items
OrganizationGrant numberCountry
Swedish Research Council2016-01065 Sweden
Swedish Energy Agency2016-011207 Sweden
Novo Nordisk FoundationNNF17OC0027698 Denmark
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Biochemistry / Year: 2021
Title: Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii .
Authors: Krska, D. / Mazurkewich, S. / Brown, H.A. / Theibich, Y. / Poulsen, J.N. / Morris, A.L. / Koropatkin, N.M. / Lo Leggio, L. / Larsbrink, J.
History
DepositionFeb 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
C: Beta-xylanase
D: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,90138
Polymers178,3094
Non-polymers2,59234
Water20,5011138
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2069
Polymers44,5771
Non-polymers6298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1418
Polymers44,5771
Non-polymers5647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,22410
Polymers44,5771
Non-polymers6479
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,33011
Polymers44,5771
Non-polymers75310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.058, 116.901, 160.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-xylanase


Mass: 44577.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor kristjanssonii (strain ATCC 700853 / DSM 12137 / I77R1B) (bacteria)
Strain: ATCC 700853 / DSM 12137 / I77R1B / Gene: Calkr_2245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E4S6E9, endo-1,4-beta-xylanase

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Non-polymers , 5 types, 1172 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M bis-tris, and 25% polyethylene glycol 3350. Protein at 51.1 mg/mL.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.88948→48.637 Å / Num. obs: 145210 / % possible obs: 97.33 % / Redundancy: 2.8 % / Biso Wilson estimate: 28.2064645318 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07681 / Net I/σ(I): 10.03
Reflection shellResolution: 1.89→1.9367 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.8267 / Num. unique obs: 13403 / CC1/2: 0.443 / % possible all: 90.96

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Auto-Rickshawphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHN

6ehn


Resolution: 1.88948348333→48.6209416022 Å / SU ML: 0.215923441482 / Cross valid method: FREE R-VALUE / σ(F): 1.34353963479 / Phase error: 21.2680332628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206762803839 2000 1.37746738846 %
Rwork0.166773559883 143194 -
obs0.167325045858 145194 97.3352372142 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1434755472 Å2
Refinement stepCycle: LAST / Resolution: 1.88948348333→48.6209416022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11892 0 169 1138 13199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006743237926912521
X-RAY DIFFRACTIONf_angle_d0.79586903162317006
X-RAY DIFFRACTIONf_chiral_restr0.05482175538281758
X-RAY DIFFRACTIONf_plane_restr0.005277722409252224
X-RAY DIFFRACTIONf_dihedral_angle_d12.87399166237160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8895-1.93670.3323602483641280.3136308434589154X-RAY DIFFRACTION88.3831651114
1.9367-1.98910.3136620055981440.26217175439510279X-RAY DIFFRACTION98.4509303863
1.9891-2.04760.2475764443111440.23626090294310342X-RAY DIFFRACTION99.4216364843
2.0476-2.11370.2602468731581440.22285393961610343X-RAY DIFFRACTION99.3651696039
2.1137-2.18930.2444847609031450.21075940600110335X-RAY DIFFRACTION99.1485335856
2.1893-2.27690.2600358488621430.19796075660410266X-RAY DIFFRACTION98.3651483651
2.2769-2.38060.2293266902781450.17933502730810377X-RAY DIFFRACTION99.3954279237
2.3806-2.50610.2325579638661450.17760128719910378X-RAY DIFFRACTION99.2361373067
2.5061-2.66310.1935972397141440.17311917135310317X-RAY DIFFRACTION98.6049580545
2.6631-2.86870.2460268446751440.18221141529310265X-RAY DIFFRACTION97.6179311638
2.8687-3.15730.2422610667071440.17391563907910352X-RAY DIFFRACTION98.2311651848
3.1573-3.6140.2018811565361420.15819968974510133X-RAY DIFFRACTION96.0100915717
3.614-4.55280.1603791708731430.12198750006410317X-RAY DIFFRACTION96.5924831471
4.5528-48.620.1408435854911450.12713388552510336X-RAY DIFFRACTION94.0084312494

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