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- PDB-6qfs: Chargeless variant of the Cellulose-binding domain from Cellulomo... -

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Basic information

Entry
Database: PDB / ID: 6qfs
TitleChargeless variant of the Cellulose-binding domain from Cellulomonas fimi
ComponentsExoglucanase/xylanase
KeywordsSUGAR BINDING PROTEIN / EXG / cellulose-binding / uncharged / Exoglucanase / xylanase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Immunoglobulin-like - #290 / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. ...Immunoglobulin-like - #290 / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ACETATE ION / Chem-ETE / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYoung, D.R. / Hoejgaard, C. / Messens, J. / Winther, J.R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Belgium
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Charge Interactions in a Highly Charge-depleted Protein
Authors: Hervo-Hansen, S. / Hojgaard, C. / Johansson, K. / Wang, Y. / Wahni, K. / Young, D. / Messens, J. / Teilum, K. / Lindorff-Larsen, K. / Winther, J.R.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Jan 24, 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: Exoglucanase/xylanase
B: Exoglucanase/xylanase
C: Exoglucanase/xylanase
D: Exoglucanase/xylanase
E: Exoglucanase/xylanase
F: Exoglucanase/xylanase
G: Exoglucanase/xylanase
H: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,43566
Polymers86,2938
Non-polymers4,14258
Water3,837213
1
A: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0005
Polymers10,7871
Non-polymers2134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2667
Polymers10,7871
Non-polymers4796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,51714
Polymers10,7871
Non-polymers73113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,62310
Polymers10,7871
Non-polymers8379
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4588
Polymers10,7871
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3729
Polymers10,7871
Non-polymers5868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1548
Polymers10,7871
Non-polymers3677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Exoglucanase/xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0445
Polymers10,7871
Non-polymers2574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.382, 137.382, 148.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11F-307-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Exoglucanase/xylanase


Mass: 10786.620 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: cex, xynB / Production host: Escherichia coli (E. coli)
References: UniProt: P07986, cellulose 1,4-beta-cellobiosidase (non-reducing end), endo-1,4-beta-xylanase

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Non-polymers , 8 types, 271 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 213 / 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

Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop
Details: 0.045 M ZnSO4 heptahydrate, 0.45 M MES monohydrate pH 6.5, 11.25% PEG monomethyl ether 550, 0.0275 M CdSO4 hydrate, 0.055 M HEPES pH 7.5, 0.55 M Na acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.2→74.27 Å / Num. obs: 82435 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Net I/σ(I): 16.5 / Num. measured all: 1163311
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2413.10.9375889945000.6870.2670.9753100
11.43-74.2712.20.04581976700.9980.0130.04747.499.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EXG

1exg


Resolution: 2.2→63.005 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.202 4107 4.99 %
Rwork0.1769 --
obs0.1782 82385 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.63 Å2 / Biso mean: 65.5308 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2.2→63.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 271 213 6545
Biso mean--75.76 56.11 -
Num. residues----841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096632
X-RAY DIFFRACTIONf_angle_d0.9859081
X-RAY DIFFRACTIONf_chiral_restr0.062992
X-RAY DIFFRACTIONf_plane_restr0.0071180
X-RAY DIFFRACTIONf_dihedral_angle_d11.4723588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.22590.37581380.349226902828
2.2259-2.2530.35871410.31826742815
2.253-2.28160.31011320.288326622794
2.2816-2.31160.2981480.276626492797
2.3116-2.34330.3171330.261226622795
2.3433-2.37670.23011460.244627122858
2.3767-2.41220.22291350.230126582793
2.4122-2.44990.25731460.216926672813
2.4499-2.49010.26321510.219526712822
2.4901-2.5330.26631240.20727122836
2.533-2.57910.2231520.188426772829
2.5791-2.62870.2641510.195226292780
2.6287-2.68230.20271340.18726912825
2.6823-2.74070.19941260.182127202846
2.7407-2.80440.22221240.172227042828
2.8044-2.87450.23241440.177326552799
2.8745-2.95230.24851570.180427002857
2.9523-3.03910.21741160.184226982814
3.0391-3.13720.24321880.180926452833
3.1372-3.24940.21171280.185426922820
3.2494-3.37940.20481270.175927332860
3.3794-3.53320.20261300.173427192849
3.5332-3.71950.22651900.171826802870
3.7195-3.95250.17111220.169527212843
3.9525-4.25760.15681310.146627192850
4.2576-4.6860.14721510.122827152866
4.686-5.36370.14631530.135227432896
5.3637-6.75650.15531460.163827852931
6.7565-63.03060.20181430.187928953038
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)
12.2805-0.6513-1.51012.3628-0.26581.2142-0.12230.9235-0.7296-0.3768-0.1947-0.17860.22870.05250.34470.32180.06320.13251.114-0.18370.74265.684938.837915.9538
20.66650.5111-0.07420.4382-0.16720.307-0.11520.96670.6006-0.18160.29620.3809-0.1325-0.06120.04520.202-0.1283-0.02161.18350.29560.6303-18.145156.035517.3526
32.87260.3542-1.57793.4158-1.04333.8440.2938-0.2390.31320.6655-0.19450.0324-0.51890.4165-0.12640.4085-0.10910.06740.55330.07770.616-12.186559.460347.1672
42.14690.961-1.21411.4103-0.04880.97220.13050.53280.54840.0278-0.2246-0.2767-0.06650.3853-0.41950.2683-0.0603-0.03350.85770.31080.678212.077464.884431.1998
53.34140.3094-0.851.25260.07050.24290.0272-0.2268-0.55730.2566-0.2075-0.22920.11930.39420.08370.33580.03680.0150.98220.31810.774127.055249.23839.6944
62.50190.0087-0.29942.1294-0.58862.0967-0.02760.831-0.3203-0.24410.00510.30990.2358-0.23760.00660.3363-0.06750.00090.76760.01780.6379-33.14941.854227.9732
72.9174-0.4784-0.34010.31660.34570.3762-0.0591-0.9118-0.86480.2287-0.2735-0.12520.18390.42040.24750.4356-0.00130.01890.88080.35730.72412.769842.529354.458
84.5156-1.3063-1.07591.74620.36922.0450.00380.4708-0.9938-0.3329-0.0707-0.41030.39490.28470.08730.5290.05930.10590.6676-0.13750.9764-8.481925.595728.9907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 106)A3 - 106
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 106)B1 - 106
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 106)C3 - 106
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 106)D1 - 106
5X-RAY DIFFRACTION5(chain 'E' and resid 3 through 106)E3 - 106
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 106)F2 - 106
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 106)G1 - 106
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 106)H1 - 106

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