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- PDB-7nwn: A carbohydrate binding module family 9 (CBM9) from Caldicellulsir... -

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Basic information

Entry
Database: PDB / ID: 7nwn
TitleA carbohydrate binding module family 9 (CBM9) from Caldicellulsiruptor kristjanssonii
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 / 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 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / S-layer homology (SLH) domain profile. / 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
DI(HYDROXYETHYL)ETHER / Beta-xylanase
Similarity search - Component
Biological speciesCaldicellulosiruptor kristjanssonii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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_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)26,19920
Polymers24,6451
Non-polymers1,55419
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-27 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.671, 172.671, 172.671
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
11AAA-479-

HOH

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Components

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Protein , 1 types, 1 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

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Non-polymers , 5 types, 159 molecules

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


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate and 40% polyethylene glycol 300
PH range: 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.97→46.191 Å / Num. obs: 31213 / % possible obs: 100 % / Redundancy: 79.9 % / CC1/2: 1 / Net I/σ(I): 26.81
Reflection shellResolution: 1.97→2.11 Å / Num. unique obs: 5694 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8U

1i8u


Resolution: 1.97→46.191 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.162 / SU B: 2.956 / SU ML: 0.08 / Average fsc free: 0.9379 / Average fsc overall: 0.949 / Average fsc work: 0.9496 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.115 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2301 1519 4.868 %
Rwork0.1804 29687 -
all0.183 --
obs-31206 99.962 %
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: 46.697 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 97 140 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121736
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.652326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8315204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33623.0399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6891511
X-RAY DIFFRACTIONr_chiral_restr0.1230.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021324
X-RAY DIFFRACTIONr_nbd_refined0.220.2782
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.213
X-RAY DIFFRACTIONr_mcbond_it4.4834.275804
X-RAY DIFFRACTIONr_mcangle_it6.2826.3921012
X-RAY DIFFRACTIONr_scbond_it5.844.801932
X-RAY DIFFRACTIONr_scangle_it7.4186.8961314
X-RAY DIFFRACTIONr_lrange_it10.3861.6642694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.3481070.2922155X-RAY DIFFRACTION99.8676
2.021-2.0770.3181180.2792112X-RAY DIFFRACTION100
2.077-2.1370.2781100.2532068X-RAY DIFFRACTION100
2.137-2.2030.282930.2472009X-RAY DIFFRACTION99.9524
2.203-2.2750.254920.2511953X-RAY DIFFRACTION100
2.275-2.3550.2381120.2171856X-RAY DIFFRACTION100
2.355-2.4430.276860.2081846X-RAY DIFFRACTION100
2.443-2.5430.27840.191765X-RAY DIFFRACTION100
2.543-2.6560.199980.1811678X-RAY DIFFRACTION100
2.656-2.7860.229920.1721593X-RAY DIFFRACTION100
2.786-2.9360.248670.1651539X-RAY DIFFRACTION100
2.936-3.1140.227670.1791469X-RAY DIFFRACTION100
3.114-3.3290.196690.181375X-RAY DIFFRACTION100
3.329-3.5960.213680.1791273X-RAY DIFFRACTION100
3.596-3.9390.189660.1551183X-RAY DIFFRACTION100
3.939-4.4030.181540.1351089X-RAY DIFFRACTION100
4.403-5.0830.212470.128973X-RAY DIFFRACTION100
5.083-6.2230.228520.161826X-RAY DIFFRACTION100
6.223-8.7890.3340.204659X-RAY DIFFRACTION100
8.789-46.1910.268140.234403X-RAY DIFFRACTION98.1177

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