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- PDB-6rs6: X-ray crystal structure of LsAA9B -

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Basic information

Entry
Database: PDB / ID: 6rs6
TitleX-ray crystal structure of LsAA9B
ComponentsAA9
KeywordsUNKNOWN FUNCTION / Fungal / family AA9
Function / homologyCoagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / GLYCINE / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER / SERINE
Function and homology information
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFrandsen, K.E.H. / Tovborg, M. / Poulsen, J.C.N. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, France, 7items
OrganizationGrant numberCountry
Danish Agency for Science Technology and Innovation12-134922 Denmark
Danish Agency for Science Technology and Innovation12-134923 Denmark
Novo Nordisk FoundationNNF17SA0027704 Denmark
European Communitys Seventh Framework ProgrammeBioStruct-X (grant agreement N283570) Denmark
European CommissionCF16-0673 - The Carlsberg Foundation Denmark
European CommissionCF17-0533 - The Carlsberg Foundation Denmark
European CommissionAgreenSkills+ (Marie-Curie FP7 COFUND People Programme under grant agreement 609398) France
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases.
Authors: Frandsen, K.E.H. / Tovborg, M. / Jorgensen, C.I. / Spodsberg, N. / Rosso, M.N. / Hemsworth, G.R. / Garman, E.F. / Grime, G.W. / Poulsen, J.N. / Batth, T.S. / Miyauchi, S. / Lipzen, A. / ...Authors: Frandsen, K.E.H. / Tovborg, M. / Jorgensen, C.I. / Spodsberg, N. / Rosso, M.N. / Hemsworth, G.R. / Garman, E.F. / Grime, G.W. / Poulsen, J.N. / Batth, T.S. / Miyauchi, S. / Lipzen, A. / Daum, C. / Grigoriev, I.V. / Johansen, K.S. / Henrissat, B. / Berrin, J.G. / Lo Leggio, L.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity_src_gen / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.pdbx_auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AA9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4389
Polymers23,2391
Non-polymers1,1998
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-3 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.190, 72.480, 78.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AA9


Mass: 23238.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold)

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
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 , 5 types, 221 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) Polyethylene glycol monomethyl ether 500 10%(w/v) Polyethylene glycol 20.000 0.1 M Imidazole/MES (pH6.5) 0.02 M Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic).
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 27139 / % possible obs: 99.6 % / Redundancy: 7.83 % / CC1/2: 0.998 / Rrim(I) all: 0.108 / Net I/σ(I): 14.07
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.01 % / Mean I/σ(I) obs: 2.74 / Num. unique obs: 4369 / CC1/2: 0.764 / Rrim(I) all: 0.678 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EJA

3eja


Resolution: 1.6→19.93 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.44 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18219 1384 5.1 %RANDOM
Rwork0.1367 ---
obs0.13903 25765 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20 Å2
2--0.26 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 76 215 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141776
X-RAY DIFFRACTIONr_bond_other_d00.0171561
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.7072438
X-RAY DIFFRACTIONr_angle_other_deg0.9681.6833665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84324.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.46815234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.195154
X-RAY DIFFRACTIONr_chiral_restr0.060.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
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_it0.9791.278902
X-RAY DIFFRACTIONr_mcbond_other0.981.275901
X-RAY DIFFRACTIONr_mcangle_it1.3541.9061124
X-RAY DIFFRACTIONr_mcangle_other1.3531.911125
X-RAY DIFFRACTIONr_scbond_it1.52874
X-RAY DIFFRACTIONr_scbond_other1.519874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0521315
X-RAY DIFFRACTIONr_long_range_B_refined2.6131943
X-RAY DIFFRACTIONr_long_range_B_other2.6121944
X-RAY DIFFRACTIONr_rigid_bond_restr4.56131741
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded9.55351689
LS refinement shellResolution: 1.6→1.697 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.275 237 -
Rwork0.22 3985 -
obs--98.44 %

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