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

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Basic information

Entry
Database: PDB / ID: 4xwm
TitleComplex structure of catalytic domain of Clostridium Cellulovorans Exgs and Cellobiose
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 / alpha-cellobiose / Exoglucanase S
Similarity search - Component
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 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: 4KKF
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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_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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0637
Polymers75,8931
Non-polymers1,1696
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint3 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.140, 109.140, 182.145
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-919-

HOH

21A-922-

HOH

31A-949-

HOH

Detailsbiological unit is the same as asym.

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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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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-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: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
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

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Non-polymers , 3 types, 600 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 597 / 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: 67.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, SODIUM TARTRATE

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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
ADSC QUANTUM 3152CCDFeb 9, 2009MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2-COOLED DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2SINGLE CRYSTAL Si(111) BENT monochromotorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 1.7→30 Å / Num. obs: 119873 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.088 / Net I/av σ(I): 34.305 / Net I/σ(I): 18.4 / Num. measured all: 791443
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.265 / Num. unique all: 12315 / Χ2: 1.004 / Rejects: 0 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
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: 1.703→27.505 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.92 / Stereochemistry target values: ML / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.1631 2000 1.67 %Random selection
Rwork0.1457 117727 --
obs0.146 119727 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.72 Å2 / Biso mean: 14.4654 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: final / Resolution: 1.703→27.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 75 601 5646
Biso mean--30.99 25.44 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085431
X-RAY DIFFRACTIONf_angle_d1.1867461
X-RAY DIFFRACTIONf_chiral_restr0.058772
X-RAY DIFFRACTIONf_plane_restr0.007959
X-RAY DIFFRACTIONf_dihedral_angle_d14.4541967
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 (%)
1.7029-1.74550.17031400.1538257839799
1.7455-1.79270.19351430.15183718514100
1.7927-1.84540.16181410.150783358476100
1.8454-1.9050.16491420.139783378479100
1.905-1.97310.15151410.139983438484100
1.9731-2.0520.15561430.136983678510100
2.052-2.14540.16181420.136884068548100
2.1454-2.25840.161430.141683968539100
2.2584-2.39990.17891420.143383738515100
2.3999-2.5850.17171440.153584438587100
2.585-2.84490.17821440.155584688612100
2.8449-3.2560.17671430.15528451859499
3.256-4.10010.14331440.13598494863899
4.1001-27.50910.15251480.1488686883497
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)
11.28060.22010.81050.62670.69371.6025-0.01430.09060.0115-0.0760.0463-0.0797-0.10990.1849-0.03310.0532-0.01740.00980.09730.01750.079417.080825.9649-31.2075
20.74990.490.48111.03480.64082.20870.03170.0464-0.0686-0.0370.0245-0.10610.10590.1201-0.04910.02770.0081-0.0090.09640.00160.087111.942814.9444-28.6382
30.77460.1980.11060.58670.13380.4156-0.0081-0.11930.04360.06460.02620.00830.0218-0.0054-0.01910.06780.0085-0.0140.110.00990.06072.817323.1142-6.3492
40.5343-0.11930.10880.3357-0.10260.5716-0.0024-0.0108-0.0227-0.0027-0.00090.0169-0.0105-0.02410.00170.0413-0.0062-0.01230.0640.00080.0603-8.159220.51-24.707
54.47040.1144-1.94480.3831-0.05631.8540.18780.05250.3675-0.0583-0.00110.0217-0.2292-0.0456-0.1560.09590.0023-0.02370.08190.02620.1051-8.770238.1032-36.2506
60.46780.1510.55760.22520.29961.324-0.06840.04550.1144-0.04920.01360.0063-0.20190.09020.06590.0817-0.0018-0.00210.07390.01120.10028.336734.5068-30.4035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 45 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 82 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 220 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 440 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 441 through 485 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 486 through 627 )A0

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