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- PDB-3acf: Crystal Structure of Carbohydrate-Binding Module Family 28 from C... -

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Basic information

Entry
Database: PDB / ID: 3acf
TitleCrystal Structure of Carbohydrate-Binding Module Family 28 from Clostridium josui Cel5A in a ligand-free form
ComponentsBeta-1,4-endoglucanase
KeywordsHYDROLASE / beta-jellyroll / cellulose-binding domain / Glycosidase
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like ...Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium josui (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTsukimoto, K. / Takada, R. / Araki, Y. / Suzuki, K. / Karita, S. / Wakagi, T. / Shoun, H. / Watanabe, T. / Fushinobu, S.
CitationJournal: Febs Lett. / Year: 2010
Title: Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module.
Authors: Tsukimoto, K. / Takada, R. / Araki, Y. / Suzuki, K. / Karita, S. / Wakagi, T. / Shoun, H. / Watanabe, T. / Fushinobu, S.
History
DepositionJan 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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_ref_seq_dif / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_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

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Assembly

Deposited unit
A: Beta-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5263
Polymers22,3901
Non-polymers1362
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.164, 63.305, 71.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-1,4-endoglucanase / Carbohydrate-Binding Module Family 28


Mass: 22390.189 Da / Num. of mol.: 1 / Fragment: UNP residues 560-752
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium josui (bacteria) / Gene: celA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q59290, cellulase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG MME 2000, (NH4)2SO4, Na-acetate, pH 4.6, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28716 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.066 / Net I/σ(I): 34.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.217 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uWW

1uww


Resolution: 1.6→28.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.319 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1460 5.1 %RANDOM
Rwork0.156 ---
obs0.158 28658 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.47 Å2 / Biso mean: 21.684 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.08 Å0.077 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 6 322 1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221530
X-RAY DIFFRACTIONr_angle_refined_deg2.4081.9522085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1465192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57724.76263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94315248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.793156
X-RAY DIFFRACTIONr_chiral_restr0.1850.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211152
X-RAY DIFFRACTIONr_mcbond_it1.4531.5962
X-RAY DIFFRACTIONr_mcangle_it2.43721556
X-RAY DIFFRACTIONr_scbond_it4.0013568
X-RAY DIFFRACTIONr_scangle_it5.9644.5529
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 103 -
Rwork0.162 1927 -
all-2030 -
obs--96.25 %

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