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- PDB-4d7u: The structure of the catalytic domain of NcLPMO9C from the filame... -

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Basic information

Entry
Database: PDB / ID: 4d7u
TitleThe structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa
ComponentsENDOGLUCANASE II
KeywordsOXIDOREDUCTASE / LYTIC MONOOXYGENASE / HEMICELLULOSE ACTIVE / AA9
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic 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) / 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 / Endoglucanase II
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBorisova, A.S. / Isaksen, T. / Mathiesen, G. / Sorlie, M. / Sandgren, M. / Eijsink, V.G.H. / Dimarogona, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity
Authors: Borisova, A.S. / Isaksen, T. / Dimarogona, M. / Kognole, A.A. / Mathiesen, G. / Varnai, A. / Rohr, A.K. / Payne, C. / Sorlie, M. / Sandgren, M. / Eijsink, V.G.H. / Sorlie, M.
History
DepositionNov 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE II
B: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2789
Polymers46,6902
Non-polymers5887
Water10,052558
1
A: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5934
Polymers23,3451
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6855
Polymers23,3451
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.258, 66.755, 66.077
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE II / NCLPMO9C-N


Mass: 23345.139 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 17-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Strain: OR74A / Plasmid: PPINK-GAPHC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): PICHIAPINK STRAIN4 / References: UniProt: Q7SHI8
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 5.1 / Details: 0.2M AMMONIUM CITRATE, 20% PEG 3350, PH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→64.81 Å / Num. obs: 49150 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.5
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 / % possible all: 29.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EIR

4eir


Resolution: 1.56→64.805 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.764 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 2423 5.02 %RANDOM
Rwork0.1563 ---
obs0.158 48932 91.057 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.496 Å2
Baniso -1Baniso -2Baniso -3
1--1.209 Å20 Å2-0.206 Å2
2--2.347 Å20 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 1.56→64.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 32 558 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193511
X-RAY DIFFRACTIONr_bond_other_d0.0010.023238
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9384794
X-RAY DIFFRACTIONr_angle_other_deg0.7183.0027480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9825.878131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.067154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined0.2240.21236
X-RAY DIFFRACTIONr_nbd_other0.1550.271
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21765
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0490.22
X-RAY DIFFRACTIONr_metal_ion_refined0.050.24
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_it0.6161.2651892
X-RAY DIFFRACTIONr_mcbond_other0.6161.2641891
X-RAY DIFFRACTIONr_mcangle_it1.1081.8952386
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6071.2651619
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0061.8762408
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 71 -
Rwork0.248 1462 -
obs--38.566 %

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