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- PDB-7nwq: A carbohydrate binding module family 9 (CBM9) from Caldicellulosi... -

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Basic information

Entry
Database: PDB / ID: 7nwq
TitleA carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjanssonii in complex with cellotriose
ComponentsBeta-xylanase
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE
Function / homology
Function and homology information


carboxylic ester hydrolase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan 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 ...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
beta-cellotriose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta-xylanase
Similarity search - Component
Biological speciesCaldicellulosiruptor kristjanssonii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.231 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
DepositionMar 17, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,11024
Polymers24,6451
Non-polymers2,46523
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-19 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.490, 172.490, 172.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11BBB-2-

BGC

21AAA-471-

HOH

31AAA-494-

HOH

41AAA-498-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein Beta-xylanase


Mass: 24645.232 Da / Num. of mol.: 1
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
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 133 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.8 Å3/Da / Density % sol: 74.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate-citrate and 40% polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→70.52 Å / Num. obs: 21538 / % possible obs: 99.6 % / Redundancy: 71.8 % / CC1/2: 1 / Net I/σ(I): 26.89
Reflection shellResolution: 2.23→2.29 Å / Num. unique obs: 1498 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i8u

1i8u


Resolution: 2.231→70.518 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.168 / SU B: 4.034 / SU ML: 0.097 / Average fsc free: 0.9448 / Average fsc overall: 0.956 / Average fsc work: 0.9572 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.162 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2258 2000 9.29 %
Rwork0.1853 19528 -
all0.189 --
obs-21528 99.657 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.231→70.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 158 111 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121787
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6752381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9965202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8423.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03615269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021315
X-RAY DIFFRACTIONr_nbd_refined0.2330.2794
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2108
X-RAY DIFFRACTIONr_metal_ion_refined0.120.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2770.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.223
X-RAY DIFFRACTIONr_mcbond_it4.113.763799
X-RAY DIFFRACTIONr_mcangle_it6.1355.6111004
X-RAY DIFFRACTIONr_scbond_it5.8264.358988
X-RAY DIFFRACTIONr_scangle_it7.8976.1791377
X-RAY DIFFRACTIONr_lrange_it12.42452.9752623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.231-2.2890.6321380.5691350X-RAY DIFFRACTION95.3846
2.289-2.3520.3381420.291375X-RAY DIFFRACTION100
2.352-2.420.3471370.2671348X-RAY DIFFRACTION100
2.42-2.4950.2951340.2341315X-RAY DIFFRACTION100
2.495-2.5760.2251330.1981286X-RAY DIFFRACTION100
2.576-2.6670.2531240.1911222X-RAY DIFFRACTION100
2.667-2.7670.2141230.1711191X-RAY DIFFRACTION100
2.767-2.880.2351170.1641148X-RAY DIFFRACTION100
2.88-3.0080.2111140.1621104X-RAY DIFFRACTION100
3.008-3.1550.2091070.1711059X-RAY DIFFRACTION100
3.155-3.3260.241040.1841015X-RAY DIFFRACTION100
3.326-3.5270.209980.184953X-RAY DIFFRACTION100
3.527-3.770.211930.171904X-RAY DIFFRACTION100
3.77-4.0720.201860.145848X-RAY DIFFRACTION100
4.072-4.460.179810.121780X-RAY DIFFRACTION100
4.46-4.9860.154740.116719X-RAY DIFFRACTION100
4.986-5.7560.163650.145645X-RAY DIFFRACTION100
5.756-7.0450.212560.19547X-RAY DIFFRACTION100
7.045-9.9470.226460.237443X-RAY DIFFRACTION100
9.947-70.5180.376280.371276X-RAY DIFFRACTION99.3464

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