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- PDB-3h3k: Structure of A. acidocaldarius cellulase CelA in complex with cel... -

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Basic information

Entry
Database: PDB / ID: 3h3k
TitleStructure of A. acidocaldarius cellulase CelA in complex with cellotetraose
ComponentsCellulase
KeywordsHYDROLASE / GH9 fold in CAZY database / Glycosidase
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / Endoglucanase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorera, S. / Eckert, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of A. acidocaldarius endoglucanase Cel9A in complex with Cello-oligosaccharides: strong -1 and -2 subsites mimic cellobiohydrolase activity
Authors: Eckert, K. / Vigouroux, A. / Lo Leggio, L. / Morera, S.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 1, 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: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2207
Polymers59,0311
Non-polymers1,1896
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.090, 129.300, 49.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellulase


Mass: 59030.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Gene: celA / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star DE3 / References: UniProt: Q9AJS0, cellulase

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 173 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% MPD, 100mM Hepes, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2008 / Details: kirkpatrick baez
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 32389 / Num. obs: 31580 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4963 / % possible all: 96.3

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GZK

3gzk


Resolution: 2.1→30.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.858 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21727 1578 5 %RANDOM
Rwork0.18649 ---
obs0.18805 29997 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.041 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 75 169 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214285
X-RAY DIFFRACTIONr_bond_other_d0.0010.022840
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9665868
X-RAY DIFFRACTIONr_angle_other_deg1.00536851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89922.642193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0341534
X-RAY DIFFRACTIONr_chiral_restr0.0880.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02906
X-RAY DIFFRACTIONr_nbd_refined0.1960.2903
X-RAY DIFFRACTIONr_nbd_other0.1840.22906
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22078
X-RAY DIFFRACTIONr_nbtor_other0.0870.22102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2180
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.28
X-RAY DIFFRACTIONr_mcbond_it0.5811.52720
X-RAY DIFFRACTIONr_mcbond_other0.081.51053
X-RAY DIFFRACTIONr_mcangle_it0.99724227
X-RAY DIFFRACTIONr_scbond_it1.19631817
X-RAY DIFFRACTIONr_scangle_it1.9454.51641
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 111 -
Rwork0.251 2122 -
obs--100 %

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