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- PDB-5o2x: Extended catalytic domain of H. jecorina LPMO9A a.k.a EG4 -

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Basic information

Entry
Database: PDB / ID: 5o2x
TitleExtended catalytic domain of H. jecorina LPMO9A a.k.a EG4
ComponentsGlycoside hydrolase family 61
KeywordsOXIDOREDUCTASE / Lytic polysaccharide monooxygenase Trichoderma reesei EG4
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / hydrolase activity / extracellular region
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Coagulation Factor XIII; Chain A, domain 1 ...Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / alpha-D-mannopyranose / Glycoside hydrolase family 61
Similarity search - Component
Biological speciesTrichoderma reesei QM6a (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsHansson, H. / Karkehabadi, S. / Mikkelsen, N.E. / Sandgren, M. / Kelemen, B. / Kaper, T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: High-resolution structure of a lytic polysaccharide monooxygenase from Hypocrea jecorina reveals a predicted linker as an integral part of the catalytic domain.
Authors: Hansson, H. / Karkehabadi, S. / Mikkelsen, N. / Douglas, N.R. / Kim, S. / Lam, A. / Kaper, T. / Kelemen, B. / Meier, K.K. / Jones, S.M. / Solomon, E.I. / Sandgren, M.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 61
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,62922
Polymers26,1331
Non-polymers3,49621
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-8 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 61.550, 47.780
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside hydrolase family 61


Mass: 26132.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First residue (histidine) is methylated: 4-METHYL-HISTIDINE (=>HIC)
Source: (gene. exp.) Trichoderma reesei QM6a (fungus) / Gene: cel61a, TRIREDRAFT_73643 / Production host: Trichoderma reesei RUT C-30 (fungus) / References: UniProt: G0R6T8

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Sugars , 2 types, 17 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 376 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.6M AmSO4 0.1M Citric Acid pH 4.0 / Temp details: ambient room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972425 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 0.95→44.3 Å / Num. obs: 121945 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.78 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Rrim(I) all: 0.083 / Net I/σ(I): 14.1
Reflection shellResolution: 0.9→0.95 Å / Rmerge(I) obs: 0.679 / Rpim(I) all: 0.375 / Rrim(I) all: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSNov. 2013data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→44.29 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.508 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12741 6451 5 %RANDOM
Rwork0.1152 ---
obs0.11582 121945 89.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.07 Å2
2---0.25 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 0.95→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 209 372 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022353
X-RAY DIFFRACTIONr_bond_other_d0.0030.022061
X-RAY DIFFRACTIONr_angle_refined_deg1.8322.0743295
X-RAY DIFFRACTIONr_angle_other_deg1.38634848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6235.085294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93226.2282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.23615283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.443151
X-RAY DIFFRACTIONr_chiral_restr0.110.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212526
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.660.6411074
X-RAY DIFFRACTIONr_mcbond_other0.6550.641073
X-RAY DIFFRACTIONr_mcangle_it0.8920.9711359
X-RAY DIFFRACTIONr_mcangle_other0.8920.9721360
X-RAY DIFFRACTIONr_scbond_it1.4060.8121279
X-RAY DIFFRACTIONr_scbond_other1.0250.791267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2321.1511902
X-RAY DIFFRACTIONr_long_range_B_refined2.4457.262944
X-RAY DIFFRACTIONr_long_range_B_other1.7876.3052678
X-RAY DIFFRACTIONr_rigid_bond_restr2.60634414
X-RAY DIFFRACTIONr_sphericity_free23.633558
X-RAY DIFFRACTIONr_sphericity_bonded6.96854658
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 281 -
Rwork0.368 6100 -
obs--60.1 %

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