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- PDB-3amq: E134C-Cellobiose co-crystal of cellulase 12A from thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3amq
TitleE134C-Cellobiose co-crystal of cellulase 12A from thermotoga maritima
ComponentsEndo-1,4-beta-glucanase
KeywordsHYDROLASE / beta jellyroll / glucanase / cellulose
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-cellobiose / beta-D-glucopyranose / Endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCheng, Y.-S. / Ko, T.-P. / Liu, J.-R. / Guo, R.-T.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima
Authors: Cheng, Y.-S. / Ko, T.-P. / Wu, T.-H. / Ma, Y. / Huang, C.-H. / Lai, H.-L. / Wang, A.H.-J. / Liu, J.-R. / Guo, R.-T.
History
DepositionAug 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
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: Endo-1,4-beta-glucanase
B: Endo-1,4-beta-glucanase
C: Endo-1,4-beta-glucanase
D: Endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,92411
Polymers123,0154
Non-polymers1,9107
Water18,2851015
1
A: Endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2763
Polymers30,7541
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2763
Polymers30,7541
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2763
Polymers30,7541
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0962
Polymers30,7541
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)230.896, 46.907, 116.409
Angle α, β, γ (deg.)90.00, 114.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-974-

HOH

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Components

#1: Protein
Endo-1,4-beta-glucanase / cellulase 12A


Mass: 30753.639 Da / Num. of mol.: 4 / Mutation: E134C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Genus: celA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60032, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALL CELLOBIOSE MOLECULES HAVE THE ALPHA-ANOMERIC CONFIGURATION AT THE C1' IN THIS STRUCTURES. THEY ...ALL CELLOBIOSE MOLECULES HAVE THE ALPHA-ANOMERIC CONFIGURATION AT THE C1' IN THIS STRUCTURES. THEY MAY REPRESENT INTERMEDIATE-LIKE STRUCTURES.

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M ammonium sulfate, 0.1M Bis-Tris, 5% glycerol, 18% PEG3350, 10mM cellobiose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 106050 / Num. obs: 104758 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 43.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 94.1

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AMN

3amn


Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 5060 random
Rwork0.19 --
all0.195 106172 -
obs0.195 100096 -
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 128 1015 9533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.02

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