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- PDB-4xwn: Complex structure of catalytic domain of Clostridium Cellulovoran... -

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Basic information

Entry
Database: PDB / ID: 4xwn
TitleComplex structure of catalytic domain of Clostridium Cellulovorans Exgs and Cellotetraose
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
beta-cellobiose / beta-cellopentaose / Exoglucanase S
Similarity search - Component
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.884 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: 4KKK
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)77,1455
Polymers75,8931
Non-polymers1,2514
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint2 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.856, 108.856, 182.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#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)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.8 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG6000, HEPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONNSRRC BL13C121
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 11, 2009MONOCHROMATOR; MIRROR
ADSC QUANTUM 3152CCDFeb 9, 2009MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2-COOLED DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2CRYSTAL SI(111) BENT MONOCHROMATORSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2.88→30 Å / Num. obs: 25404 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.94 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.161 / Net I/av σ(I): 25.328 / Net I/σ(I): 14.6 / Num. measured all: 172053
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.252 / Num. unique all: 2715 / Χ2: 1.054 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata reduction
PHASER2.5.3phasing
RESOLVE2.15phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F9O

1f9o


Resolution: 2.884→26.475 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.05 / Stereochemistry target values: ML / Details: TLS
RfactorNum. reflection% reflection
Rfree0.1929 1998 7.89 %
Rwork0.1636 23332 -
obs0.1659 25330 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.74 Å2 / Biso mean: 34.1304 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 2.884→26.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 81 27 5120
Biso mean--45.48 27.6 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065265
X-RAY DIFFRACTIONf_angle_d1.1077157
X-RAY DIFFRACTIONf_chiral_restr0.049727
X-RAY DIFFRACTIONf_plane_restr0.007915
X-RAY DIFFRACTIONf_dihedral_angle_d13.5921797
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 (%)
2.884-2.9560.25021400.217216411781100
2.956-3.03580.26741400.224516261766100
3.0358-3.1250.25051410.223516441785100
3.125-3.22570.24641410.209716461787100
3.2257-3.34080.23331400.216321772100
3.3408-3.47430.24321390.196716361775100
3.4743-3.6320.23111430.17416661809100
3.632-3.8230.18881400.165416411781100
3.823-4.06170.17561440.136916751819100
4.0617-4.3740.13631400.135816561796100
4.374-4.81180.16781450.123716791824100
4.8118-5.50260.15351440.13516871831100
5.5026-6.91230.16231470.140917111858100
6.9123-26.47570.16811540.15091792194698
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)
12.0747-0.30960.34081.78050.34133.85970.11360.15370.0226-0.1490.0729-0.3231-0.01510.2391-0.16850.1603-0.02590.03430.293-0.00450.283616.587424.3626-32.7892
21.07970.03920.01820.62550.17250.65920.0535-0.2235-0.10470.1271-0.0348-0.07890.09670.04-0.02210.2043-0.009-0.02710.29770.06640.26314.046319.0866-14.4506
31.0316-0.0520.44920.9029-0.06521.4729-0.0456-0.1153-0.05440.00860.0070.0483-0.0037-0.14910.03190.1821-0.0208-0.01140.28120.01710.2509-10.832223.0368-23.7515
48.61080.4401-4.3881.3997-0.43365.1070.32390.25010.4526-0.18-0.0260.1665-0.5296-0.15-0.28720.27510.0087-0.06470.20820.03760.2582-8.26737.9522-36.6892
51.91420.70.68531.11590.61621.4433-0.11320.2386-0.0428-0.16950.0741-0.1696-0.22340.11910.03720.2654-0.01520.02160.24990.05160.21923.580831.1319-42.0566
61.23390.7071.05241.80611.64824.3357-0.0771-0.03020.1598-0.10510.0307-0.1183-0.37920.1950.02280.18380.0065-0.00510.22750.01760.317412.679237.1036-20.3524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 45 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 263 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 440 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 441 through 485 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 486 through 552 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 553 through 629 )A0

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