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- PDB-4el8: The unliganded structure of C.bescii CelA GH48 module -

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Basic information

Entry
Database: PDB / ID: 4el8
TitleThe unliganded structure of C.bescii CelA GH48 module
ComponentsGlycoside hydrolase family 48
KeywordsHYDROLASE / (A/A)6 BARRE / CelA / GH48 / glycoside hydrolase
Function / homology
Function and homology information


cellulose binding / cellulase / 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 / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. ...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 / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / CBM2/CBM3, carbohydrate-binding domain superfamily / 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
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Science / Year: 2013
Title: Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA.
Authors: Brunecky, R. / Alahuhta, M. / Xu, Q. / Donohoe, B.S. / Crowley, M.F. / Kataeva, I.A. / Yang, S.J. / Resch, M.G. / Adams, M.W. / Lunin, V.V. / Himmel, M.E. / Bomble, Y.J.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4364
Polymers72,2381
Non-polymers1983
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.300, 57.666, 106.060
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

21A-1053-

HOH

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Components

#1: Protein Glycoside hydrolase family 48


Mass: 72238.273 Da / Num. of mol.: 1 / Fragment: UNP residues 1126-1759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (bacteria) / Strain: DSM 6725 / Z-1320 / Gene: Athe_1867 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKU7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CARBOHYDRATE MODULE IS MISSING FROM THE STRUCTURE ALTHOUGH IT WAS PART OF THE CONSTRUCT. THE ...THE CARBOHYDRATE MODULE IS MISSING FROM THE STRUCTURE ALTHOUGH IT WAS PART OF THE CONSTRUCT. THE AUTHORS BELIEVE THAT IT GOT CLEAVED DURING CRYSTALLIZATION

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Tri-sodium citrate pH 5.8 and 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 10, 2010 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→51.81 Å / Num. all: 25544 / Num. obs: 25544 / % possible obs: 100 % / Redundancy: 8.72 % / Rsym value: 0.1195 / Net I/σ(I): 13.57
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.17 / Num. unique all: 2604 / Rsym value: 0.5155 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MrBUMPphasing
REFMAC5.6.0117refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G9G

1g9g


Resolution: 2.45→51.81 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.702 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25812 1287 5 %RANDOM
Rwork0.1954 ---
obs0.1986 24231 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.328 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å2-0.24 Å2
2--0.94 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.45→51.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 10 254 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025338
X-RAY DIFFRACTIONr_bond_other_d0.0010.023604
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9177276
X-RAY DIFFRACTIONr_angle_other_deg0.98738696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17723.908261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47915801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0011519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021236
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 78 -
Rwork0.311 1731 -
obs-78 99.23 %

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