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- PDB-4l6x: Crystal Structure of a GH48 cellobiohydrolase from Caldicellulosi... -

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Basic information

Entry
Database: PDB / ID: 4l6x
TitleCrystal Structure of a GH48 cellobiohydrolase from Caldicellulosiruptor bescii
ComponentsGlycoside hydrolase family 48
KeywordsHydrolase / sugar binding protein / Cellobiohydrolase / Processive
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 / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / CBM2/CBM3, carbohydrate-binding 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
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJiao, A. / Bai, A. / Yan, F. / Geng, W.
CitationJournal: to be published
Title: Crystallization and preliminary X-ray analysis of a processive cellobiohydrolase CbCBH48A from Caldicellulosiruptor bescii
Authors: Jiao, A. / Bai, A. / Yan, F. / Geng, W.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)74,7473
Polymers74,6231
Non-polymers1242
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.123, 57.562, 106.469
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycoside hydrolase family 48


Mass: 74622.898 Da / Num. of mol.: 1 / Fragment: unp residues 1122-1759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (bacteria) / Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_1867 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: B9MKU7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG 4000,0.1 M Tris-Bis,18% 2-Propanol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 1 Å
DetectorDetector: CCD / Date: May 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 75252 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.767.30.405199.9
1.76-1.837.40.328199.9
1.83-1.917.40.2421100
1.91-2.027.40.174199.9
2.02-2.147.40.138199.9
2.14-2.317.40.12199.9
2.31-2.547.40.1041100
2.54-2.917.30.066199.8
2.91-3.6670.037199.6
3.66-506.60.029196.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.83 / SU B: 6.595 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23335 3730 5 %RANDOM
Rwork0.21627 ---
obs0.21713 70407 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0.29 Å2
2--1.56 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 8 216 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025258
X-RAY DIFFRACTIONr_bond_other_d0.0050.024640
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9197151
X-RAY DIFFRACTIONr_angle_other_deg0.726310701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99123.953258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28615791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4591519
X-RAY DIFFRACTIONr_chiral_restr0.0570.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021323
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_it0.261.2182507
X-RAY DIFFRACTIONr_mcbond_other0.261.2182506
X-RAY DIFFRACTIONr_mcangle_it0.4891.8263132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.141.2242751
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 276 -
Rwork0.292 4996 -
obs--94.73 %
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)
10.3558-0.0680.01180.44750.51643.6373-0.0272-0.0510.0540.13410.0439-0.03350.65980.0223-0.01670.16210.0542-0.00330.061-0.00910.12123.95790.654925.6586
20.37960.03750.19130.49960.42323.7369-0.0003-0.04690.04850.08070.0132-0.02820.3534-0.0646-0.01290.08110.03940.0030.0712-0.00890.13882.53645.544224.4305
339.8464-24.4116-11.10117.02358.06113.8606-0.15920.1030.05270.1430.15380.00220.07170.10160.00540.06170.03960.03160.12290.05360.0366-3.09526.453930.3388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 637
2X-RAY DIFFRACTION2A801 - 1016
3X-RAY DIFFRACTION3A702

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