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- PDB-2yet: Thermoascus GH61 isozyme A -

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Basic information

Entry
Database: PDB / ID: 2yet
TitleThermoascus GH61 isozyme A
ComponentsGH61 ISOZYME A
KeywordsHYDROLASE / DEGRADATION OF BIOMASS
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / : / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETYL GROUP / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesTHERMOASCUS AURANTIACUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsOtten, H. / Quinlan, R.J. / Sweeney, M.D. / Poulsen, J.-C.N. / Johansen, K.S. / Krogh, K.B.R.M. / Joergensen, C.I. / Tovborg, M. / Anthonsen, A. / Tryfona, T. ...Otten, H. / Quinlan, R.J. / Sweeney, M.D. / Poulsen, J.-C.N. / Johansen, K.S. / Krogh, K.B.R.M. / Joergensen, C.I. / Tovborg, M. / Anthonsen, A. / Tryfona, T. / Walter, C.P. / Dupree, P. / Xu, F. / Davies, G.J. / Walton, P.H. / Lo Leggio, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Insights Into the Oxidative Degradation of Cellulose by a Copper Metalloenzyme that Exploits Biomass Components.
Authors: Quinlan, R.J. / Sweeney, M.D. / Lo Leggio, L. / Otten, H. / Poulsen, J.-C.N. / Johansen, K.S. / Krogh, K.B.R.M. / Jorgensen, C.I. / Tovborg, M. / Anthonsen, A. / Tryfona, T. / Walter, C.P. / ...Authors: Quinlan, R.J. / Sweeney, M.D. / Lo Leggio, L. / Otten, H. / Poulsen, J.-C.N. / Johansen, K.S. / Krogh, K.B.R.M. / Jorgensen, C.I. / Tovborg, M. / Anthonsen, A. / Tryfona, T. / Walter, C.P. / Dupree, P. / Xu, F. / Davies, G.J. / Walton, P.H.
History
DepositionMar 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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: GH61 ISOZYME A
B: GH61 ISOZYME A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45310
Polymers48,8362
Non-polymers6178
Water11,259625
1
A: GH61 ISOZYME A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5704
Polymers24,4181
Non-polymers1523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH61 ISOZYME A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8836
Polymers24,4181
Non-polymers4655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.404, 88.467, 70.324
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:228 )
211CHAIN B AND (RESSEQ 1:228 )

NCS oper: (Code: given
Matrix: (1, 0.004824, -0.00431), (-0.00508, 0.9981, -0.06148), (0.004005, 0.0615, 0.9981)
Vector: 7.989, 4.447, -36.39)

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein GH61 ISOZYME A


Mass: 24418.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GH61 FRAGMENT. METHYLATION AT 4-N-H1, AND TWO CYSTINES AT C56-178 AND C97-C101 IN BOTH PROTEIN CHAINS. N-ACETYLGLUCOSAMIN-GLYCOSYLATION AT N138 IN THE B CHAIN AND NOT CLEARLY VISIBLE IN CHAIN A.
Source: (gene. exp.) THERMOASCUS AURANTIACUS (fungus) / Production host: ASPERGILLUS ORYZAE (mold) / Strain (production host): JAL250 / References: UniProt: G3XAP7*PLUS, cellulase
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 632 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsLACKING THE 21 AMINO ACID SIGNAL PEPTIDE GENBANK: ACS05720.1

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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: 1.92 Å3/Da / Density % sol: 35.44 % / Description: NONE
Crystal growpH: 8
Details: 0.2 M NACL, 0.1 M HEPES, PH 8.0 AND 25%(W/V) PEG 3350. CRYO PROTECTED WITH 8%(W/V) GLYCEROL, 8%(W/V) ETHYLENE GLYCOL, 9%(W/V)D-SUCROSE AND 2%(W/V)D-GLUCOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 28, 2008
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R IS 400 M)
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.49→12.33 Å / Num. obs: 67162 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.3 / % possible all: 74.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VTC

2vtc


Resolution: 1.502→12.333 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 18.72 / Stereochemistry target values: ML
Details: RESIDUES 25-27 ARE DISORDERED IN BOTH CHAINS. THERE IS WELL DEFINED ELECTRON DENSITY FOR THE RAMACHANDRAN OUTLIERS H57 IN BOTH CHAINS. DISORDERED LOOP 25-27, MODELED IN TWO CONFORMATIONS FOR ...Details: RESIDUES 25-27 ARE DISORDERED IN BOTH CHAINS. THERE IS WELL DEFINED ELECTRON DENSITY FOR THE RAMACHANDRAN OUTLIERS H57 IN BOTH CHAINS. DISORDERED LOOP 25-27, MODELED IN TWO CONFORMATIONS FOR THE B CHAIN, GLYCOSYLATION JUST IN B CHAIN
RfactorNum. reflection% reflection
Rfree0.1851 3310 5.1 %
Rwork0.1437 --
obs0.1458 65351 92.54 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.95 Å2 / ksol: 0.556 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.3432 Å20 Å21.1554 Å2
2---3.7884 Å20 Å2
3---0.4452 Å2
Refinement stepCycle: LAST / Resolution: 1.502→12.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 34 625 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093701
X-RAY DIFFRACTIONf_angle_d1.2895104
X-RAY DIFFRACTIONf_dihedral_angle_d13.2921320
X-RAY DIFFRACTIONf_chiral_restr0.085565
X-RAY DIFFRACTIONf_plane_restr0.006680
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL0.33
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5024-1.52380.2717810.23181833X-RAY DIFFRACTION66
1.5238-1.54650.29261250.2092372X-RAY DIFFRACTION85
1.5465-1.57070.25591500.18322349X-RAY DIFFRACTION85
1.5707-1.59630.26141270.15652414X-RAY DIFFRACTION87
1.5963-1.62380.21391380.14472463X-RAY DIFFRACTION88
1.6238-1.65330.20291180.12172471X-RAY DIFFRACTION89
1.6533-1.6850.19421400.12062532X-RAY DIFFRACTION90
1.685-1.71930.1841180.11922570X-RAY DIFFRACTION92
1.7193-1.75660.21011350.1222576X-RAY DIFFRACTION93
1.7566-1.79730.19041150.12022601X-RAY DIFFRACTION92
1.7973-1.84210.1991420.12792601X-RAY DIFFRACTION94
1.8421-1.89180.18251320.13452653X-RAY DIFFRACTION94
1.8918-1.94720.20031440.14062627X-RAY DIFFRACTION95
1.9472-2.00980.19661300.13942679X-RAY DIFFRACTION95
2.0098-2.08130.17551660.14282659X-RAY DIFFRACTION96
2.0813-2.16420.19381390.14722678X-RAY DIFFRACTION97
2.1642-2.26220.17971360.14032736X-RAY DIFFRACTION97
2.2622-2.38060.18811520.14022712X-RAY DIFFRACTION97
2.3806-2.52860.16561600.14282719X-RAY DIFFRACTION97
2.5286-2.72190.16511470.15282736X-RAY DIFFRACTION98
2.7219-2.99220.2131540.15582741X-RAY DIFFRACTION98
2.9922-3.41710.18621630.14882754X-RAY DIFFRACTION98
3.4171-4.27520.15111410.13342762X-RAY DIFFRACTION99
4.2752-12.33380.15661570.14832803X-RAY DIFFRACTION98

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