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- PDB-3aof: Crystal structures of Thermotoga maritima Cel5A in complex with M... -

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Basic information

Entry
Database: PDB / ID: 3aof
TitleCrystal structures of Thermotoga maritima Cel5A in complex with Mannotriose substrate
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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.288 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
DepositionSep 27, 2010Deposition 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Mar 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)75,1193
Polymers74,6152
Non-polymers5041
Water16,286904
1
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)37,3071
Polymers37,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8122
Polymers37,3071
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.696, 77.946, 62.959
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase / Cellulase


Mass: 37307.434 Da / Num. of mol.: 2 / Mutation: E136A, W283L
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)-beta-D-mannopyranose


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


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 298 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 298K

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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: Sep 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.288→25 Å / Num. obs: 147549 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.039 / Net I/σ(I): 43.3
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 14486 / Rsym value: 0.329 / % possible all: 95.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.288→24.373 Å / SU ML: 0.14 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 7410 5.02 %
Rwork0.1724 --
obs0.1732 147539 97.31 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.585 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.551 Å20 Å20.2816 Å2
2--0.7452 Å2-0 Å2
3---0.8059 Å2
Refinement stepCycle: LAST / Resolution: 1.288→24.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 34 904 6108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045364
X-RAY DIFFRACTIONf_angle_d1.0067259
X-RAY DIFFRACTIONf_dihedral_angle_d18.9092018
X-RAY DIFFRACTIONf_chiral_restr0.072741
X-RAY DIFFRACTIONf_plane_restr0.005916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2875-1.30220.26472510.23174316X-RAY DIFFRACTION90
1.3022-1.31750.23832170.21994575X-RAY DIFFRACTION96
1.3175-1.33360.23672500.21134614X-RAY DIFFRACTION96
1.3336-1.35040.22842440.19944528X-RAY DIFFRACTION96
1.3504-1.36820.20072530.19414684X-RAY DIFFRACTION96
1.3682-1.38690.23812460.19384529X-RAY DIFFRACTION96
1.3869-1.40680.22172350.18984637X-RAY DIFFRACTION97
1.4068-1.42780.20492680.18444601X-RAY DIFFRACTION97
1.4278-1.45010.20462550.18334617X-RAY DIFFRACTION97
1.4501-1.47380.18812490.17734635X-RAY DIFFRACTION97
1.4738-1.49920.20162470.16894650X-RAY DIFFRACTION97
1.4992-1.52650.20112470.16934609X-RAY DIFFRACTION97
1.5265-1.55590.19132310.16354668X-RAY DIFFRACTION97
1.5559-1.58760.20142120.16244739X-RAY DIFFRACTION97
1.5876-1.62210.17562450.15784655X-RAY DIFFRACTION98
1.6221-1.65980.17492590.15874658X-RAY DIFFRACTION98
1.6598-1.70130.1692590.16134732X-RAY DIFFRACTION98
1.7013-1.74730.17992390.16694687X-RAY DIFFRACTION98
1.7473-1.79870.18992530.16694709X-RAY DIFFRACTION98
1.7987-1.85680.18912380.1674722X-RAY DIFFRACTION98
1.8568-1.92310.19922660.16894687X-RAY DIFFRACTION99
1.9231-2.00010.1722200.17084771X-RAY DIFFRACTION98
2.0001-2.09110.18942510.16934751X-RAY DIFFRACTION99
2.0911-2.20120.18953140.16974664X-RAY DIFFRACTION99
2.2012-2.3390.16192130.1674839X-RAY DIFFRACTION99
2.339-2.51950.17732540.17154771X-RAY DIFFRACTION99
2.5195-2.77270.20582580.18014790X-RAY DIFFRACTION99
2.7727-3.17320.18552370.17564750X-RAY DIFFRACTION99
3.1732-3.9950.16572510.16234827X-RAY DIFFRACTION99
3.995-24.3770.18732480.17194714X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 1.9296 Å / Origin y: -9.1647 Å / Origin z: -14.1257 Å
111213212223313233
T0.0533 Å2-0.0067 Å20.0123 Å2-0.0442 Å20.0004 Å2--0.0449 Å2
L0.4655 °2-0.0541 °20.2717 °2-0.1484 °2-0.0488 °2--0.3121 °2
S-0.0058 Å °0.05 Å °0.0079 Å °0.0048 Å °0.0057 Å °-0.0247 Å °-0.0094 Å °0.0241 Å °-0 Å °
Refinement TLS groupSelection details: all

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