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- PDB-8e1w: Neutron crystal structure of Panus similis AA9A at room temperature -

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Basic information

Entry
Database: PDB / ID: 8e1w
TitleNeutron crystal structure of Panus similis AA9A at room temperature
ComponentsEndo-beta-1,4-glucanase D
KeywordsOXIDOREDUCTASE / beta sandwiches / glycosylated
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesPanus similis (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeilleur, F. / Tandrup, T. / Lo Leggio, L.
Funding support Denmark, United States, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Danish Council for Independent Research8021-00273B Denmark
National Institute of Food and Agriculture (NIFA, United States)Hatch211001 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature.
Authors: Tandrup, T. / Lo Leggio, L. / Meilleur, F.
History
DepositionAug 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 2.0Jan 18, 2023Group: Atomic model / Category: atom_site
Revision 2.1Apr 3, 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: Endo-beta-1,4-glucanase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5934
Polymers25,2731
Non-polymers3203
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.469, 126.469, 126.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

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Components

#1: Protein Endo-beta-1,4-glucanase D / Endoglucanase D / Carboxymethylcellulase D / Cellulase D


Mass: 25272.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panus similis (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A0S2GKZ1, cellulase
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 1.30 M NaCl, 0.1 M citric acid

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
SPALLATION SOURCEORNL Spallation Neutron Source MANDI23.0-5.0
Detector
TypeIDDetectorDate
DECTRIS EIGER R 4M1PIXELAug 10, 2020
ORNL ANGER CAMERA2AREA DETECTORAug 8, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
231
351
Reflection

Entry-ID: 8E1W / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rpim(I) allRrim(I) allNet I/σ(I)
2.1-30.672074999.8710.30.9880.05710.185114.16
2.8-14.8894299.310.20.920.0810.27510.1
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rpim(I) allDiffraction-ID
2.8-2.920190.7460.48021
2.8-2.98690.3480.1021

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Mantiddata reduction
LAUENORMdata scaling
PHASERphasing
Refinement

SU ML: 0.2256 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.7181 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5N04

5n04

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)Diffraction-ID
2.1-30.67X-RAY DIFFRACTION33.560.17020.14840.1496103319705207384.9899.921.35
2.8-14.8NEUTRON DIFFRACTION0.25980.2251894299.31
Refinement stepCycle: LAST / Resolution: 2.1→30.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 16 117 1921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03014043
X-RAY DIFFRACTIONf_angle_d2.35666990
X-RAY DIFFRACTIONf_chiral_restr0.0728291
X-RAY DIFFRACTIONf_plane_restr0.0085731
X-RAY DIFFRACTIONf_dihedral_angle_d19.72141071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.29511440.24552750X-RAY DIFFRACTION100
2.21-2.350.24471570.19662743X-RAY DIFFRACTION100
2.35-2.530.25521120.20122806X-RAY DIFFRACTION100
2.53-2.790.24481430.17882755X-RAY DIFFRACTION100
2.79-3.190.18551700.16922794X-RAY DIFFRACTION100
3.19-4.020.13281570.1242833X-RAY DIFFRACTION99.97
4.02-30.670.11091500.10363024X-RAY DIFFRACTION99.56

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