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- PDB-3azs: Diverse Substrates Recognition Mechanism Revealed by Thermotoga m... -

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Basic information

Entry
Database: PDB / ID: 3azs
TitleDiverse Substrates Recognition Mechanism Revealed by Thermotoga maritima Cel5A Structures in Complex with Mannotriose
ComponentsEndoglucanase
KeywordsHYDROLASE / cellulose / cellulase / biofuel / Tim Barrel
Function / homology
Function and homology information


glucan exo-1,3-beta-glucosidase activity / glucan catabolic process
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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWu, 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.
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
DepositionMay 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7704
Polymers74,7612
Non-polymers1,0092
Water12,142674
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8852
Polymers37,3801
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8852
Polymers37,3801
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.730, 78.046, 62.927
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase


Mass: 37380.488 Da / Num. of mol.: 2 / Mutation: E253A
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-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M tris pH8.5 , 0.4M NaCl, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→25 Å / Num. obs: 67472 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.043 / Net I/σ(I): 30.1
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 4 % / Mean I/σ(I) obs: 10.6 / Num. unique all: 6608 / Rsym value: 0.124 / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AMC

3amc


Resolution: 1.69→25 Å / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3381 5 %
Rwork0.155 --
all-67380 -
obs-66584 -
Solvent computationBsol: 44.6583 Å2
Displacement parametersBiso mean: 15.2534 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å20.491 Å2
2---1.165 Å20 Å2
3----1.455 Å2
Refinement stepCycle: LAST / Resolution: 1.69→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 68 674 5924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1311.5
X-RAY DIFFRACTIONc_scbond_it2.2792
X-RAY DIFFRACTIONc_mcangle_it1.5912
X-RAY DIFFRACTIONc_scangle_it3.3672.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3mat_mod1.param
X-RAY DIFFRACTION4cis.param

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