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- PDB-7pqr: LsAA9A expressed in E. coli -

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Basic information

Entry
Database: PDB / ID: 7pqr
TitleLsAA9A expressed in E. coli
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / 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
ACETATE ION / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsMuderspach, S.J. / Metherall, J. / Ipsen, J. / Rollan, C.H. / Norholm, M. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Danish Council for Independent Research8021-00273B Denmark
CitationJournal: Iucrj / Year: 2022
Title: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding.
Authors: Tandrup, T. / Muderspach, S.J. / Banerjee, S. / Santoni, G. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Johansen, K.S. / Meilleur, F. / Lo Leggio, L.
History
DepositionSep 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09616
Polymers25,2601
Non-polymers83615
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-118 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.920, 48.920, 109.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Auxiliary activity 9


Mass: 25259.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0S2GKZ1

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Non-polymers , 5 types, 455 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#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.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 1.8 M ammonium sulphate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.3→48.92 Å / Num. obs: 63029 / % possible obs: 99.4 % / Redundancy: 6.14 % / CC1/2: 0.999 / Rrim(I) all: 0.077 / Net I/σ(I): 12.2
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.06 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 8661 / CC1/2: 0.482 / Rrim(I) all: 1.25 / % possible all: 93.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFeb 5, 2021 BUILT=20210323data reduction
XSCALEJan 31, 2020data scaling
MOLREP11.7.03phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACH

5ach


Resolution: 1.3→48.92 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / WRfactor Rfree: 0.1544 / WRfactor Rwork: 0.1311 / FOM work R set: 0.8694 / SU B: 0.777 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0384 / SU Rfree: 0.0405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1533 3124 5 %RANDOM
Rwork0.1333 ---
obs0.1343 59905 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.62 Å2 / Biso mean: 17.567 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20 Å2
2--0.64 Å20 Å2
3----1.29 Å2
Refinement stepCycle: final / Resolution: 1.3→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 39 463 2289
Biso mean--39.14 33.4 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131978
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171739
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.6382738
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5744011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94823.46998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.434158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022376
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02460
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 238 -
Rwork0.288 4302 -
all-4540 -
obs--97.36 %

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