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- PDB-3amg: Crystal structures of Thermotoga maritima Cel5A in complex with C... -

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Basic information

Entry
Database: PDB / ID: 3amg
TitleCrystal structures of Thermotoga maritima Cel5A in complex with Cellobiose substrate, mutant form
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / glycosyl hydrolase family 5 / cellulase / biofuel / hyperthermostable
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / beta-D-glucopyranose / Endoglucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWu, T.H. / Huang, C.H. / Ko, T.P. / Lai, H.L. / Ma, Y. / Cheng, Y.S. / Liu, J.R. / Guo, R.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Diverse substrate recognition mechanism revealed by Thermotoga maritima Cel5A structures in complex with cellotetraose, cellobiose and mannotriose
Authors: Wu, T.H. / Huang, C.H. / Ko, T.P. / Lai, H.L. / Ma, Y. / Chen, C.C. / Cheng, Y.S. / Liu, J.R. / Guo, R.T.
History
DepositionAug 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references / Derived calculations
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_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 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2834
Polymers74,7612
Non-polymers5222
Water2,216123
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5612
Polymers37,3801
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7232
Polymers37,3801
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.979, 73.356, 62.192
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase / Cellulase


Mass: 37380.488 Da / Num. of mol.: 2 / Mutation: E136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_1751 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X273, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.84 Å3/Da / Density % sol: 33.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.387→25 Å / Num. obs: 21337 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.042 / Net I/σ(I): 30.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.283 / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 985 4.6 %
Rwork0.2332 --
obs-20271 94.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.8748 Å2
Displacement parametersBiso mean: 53.6905 Å2
Baniso -1Baniso -2Baniso -3
1--10.741 Å20 Å213.677 Å2
2--0.548 Å20 Å2
3---10.193 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 35 123 5196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5331.5
X-RAY DIFFRACTIONc_scbond_it1.9572
X-RAY DIFFRACTIONc_mcangle_it2.5982
X-RAY DIFFRACTIONc_scangle_it3.0552.5
Refinement TLS params.Method: refined / Origin x: 14.7155 Å / Origin y: 1.9689 Å / Origin z: -0.1563 Å
111213212223313233
T0.2153 Å2-0.0258 Å20.0835 Å2-0.1937 Å2-0.0143 Å2--0.2594 Å2
L1.9392 °2-0.022 °22.0662 °2-0.9689 °2-0.2191 °2--3.4954 °2
S-0.016 Å °0.0284 Å °-0.0647 Å °-0.1612 Å °0.0078 Å °0.0809 Å °0.1662 Å °-0.0224 Å °-0 Å °
Refinement TLS groupSelection details: all
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3cbi_dundee.par
X-RAY DIFFRACTION4glc_dundee.par

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