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- PDB-4xwl: Catalytic domain of Clostridium Cellulovorans Exgs -

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Basic information

Entry
Database: PDB / ID: 4xwl
TitleCatalytic domain of Clostridium Cellulovorans Exgs
ComponentsExoglucanase S
KeywordsHYDROLASE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain ...Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Few Secondary Structures / Irregular / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Exoglucanase S
Similarity search - Component
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
Authorsliaw, Y.-C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structures of exoglucanase from Clostridium cellulovorans: cellotetraose binding and cleavage
Authors: Tsai, L.-C. / Amiraslanov, I. / Chen, H.R. / Chen, Y.W. / Lee, H.L. / Liang, P.H. / Liaw, Y.-C.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 28, 2015ID: 4KIH
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exoglucanase S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,61124
Polymers75,8931
Non-polymers2,71723
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint30 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.243, 108.243, 182.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-884-

HOH

21A-907-

HOH

31A-908-

HOH

41A-925-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exoglucanase S


Mass: 75893.453 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 32-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulovorans (bacteria) / Gene: exgS / Plasmid: PHTPP13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: O65986, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Non-polymers , 9 types, 492 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG400, AMMONIUM SULFATE, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2008 / Details: MONOCHROMATOR
RadiationMonochromator: LN2-COOLED DOUBLE CRYSTAL SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 68817 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.931 / Net I/av σ(I): 28.793 / Net I/σ(I): 10.6 / Num. measured all: 588718
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.401 / Num. unique all: 3755 / Χ2: 0.65 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.0phasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F9O

1f9o


Resolution: 2.051→28.332 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.64 / Stereochemistry target values: ML / Details: TLS
RfactorNum. reflection% reflection
Rfree0.1737 1999 2.92 %
Rwork0.1419 66475 -
obs0.1429 68474 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.35 Å2 / Biso mean: 26.2521 Å2 / Biso min: 12.45 Å2
Refinement stepCycle: final / Resolution: 2.051→28.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 177 472 5658
Biso mean--50.3 35.27 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085447
X-RAY DIFFRACTIONf_angle_d1.0557380
X-RAY DIFFRACTIONf_chiral_restr0.045721
X-RAY DIFFRACTIONf_plane_restr0.005946
X-RAY DIFFRACTIONf_dihedral_angle_d13.9681945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0506-2.10180.17841360.14734493462996
2.1018-2.15860.18611400.14314667480799
2.1586-2.22210.19161410.144646714812100
2.2221-2.29380.17821390.146546934832100
2.2938-2.37580.18881420.14347064848100
2.3758-2.47080.19881420.141747314873100
2.4708-2.58320.18261420.14447024844100
2.5832-2.71930.17941420.147147544896100
2.7193-2.88950.18791430.150647364879100
2.8895-3.11240.19561430.15447554898100
3.1124-3.42510.17071440.153947814925100
3.4251-3.91960.15731450.129648174962100
3.9196-4.9340.14261460.121448745020100
4.934-28.33450.17881540.14950955249100
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)
10.64710.14180.3331.42260.35661.36650.02720.0837-0.0609-0.0370.0218-0.1497-0.00540.1209-0.05120.0774-0.00130.00090.18830.00250.169514.580520.174-31.2998
20.61010.37080.15461.14420.15580.58990.0187-0.16440.0160.1133-0.00730.00240.0284-0.0419-0.00950.17020.0016-0.01660.2450.00850.172.451122.9105-6.3949
30.6078-0.19760.13310.4446-0.07610.7324-0.0037-0.0309-0.01180.0203-0.00950.0234-0.0255-0.04420.0160.1272-0.0168-0.01740.1785-0.00190.1699-8.192220.511-24.7214
47.04441.6823-4.24431.4576-1.20324.03160.18350.13880.3621-0.0456-0.00050.0874-0.2984-0.138-0.16740.14070.0212-0.04310.14090.00630.1656-8.679337.6122-36.9242
55.11852.49152.50932.39160.7661.976-0.13480.1468-0.0229-0.11880.0496-0.1126-0.19570.14040.08520.14580.02560.0350.13350.00820.12283.16529.5415-44.7495
65.83990.3434-3.29464.2638-0.22994.95140.0385-0.19170.53320.10690.0682-0.0022-0.3616-0.0796-0.09730.1427-0.0172-0.02270.1474-0.06220.202310.72541.6256-5.6789
72.97532.17312.72912.58232.3112.9754-0.21040.0210.237-0.36070.07360.02-0.5320.08180.09790.1986-0.0170.01760.18040.01830.211614.036334.9877-30.3882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 82 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 220 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 440 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 441 through 485 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 486 through 547 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 548 through 581 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 582 through 629 )A0

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