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- PDB-4d7v: The structure of the catalytic domain of NcLPMO9C from the filame... -

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Basic information

Entry
Database: PDB / ID: 4d7v
TitleThe structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa
ComponentsENDOGLUCANASE II
KeywordsOXIDOREDUCTASE / CATALYTIC DOMAIN / HEMICELLULOSE ACTIVE / AA9
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose binding / 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) / 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 - #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
ACETATE ION / AA9 family lytic polysaccharide monooxygenase C
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBorisova, A.S. / Isaksen, T. / Sandgren, M. / Sorlie, 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 1.4May 1, 2024Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.5Oct 16, 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: ENDOGLUCANASE II
B: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,73918
Polymers46,6902
Non-polymers1,04916
Water7,620423
1
A: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9039
Polymers23,3451
Non-polymers5588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDOGLUCANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8379
Polymers23,3451
Non-polymers4918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.308, 67.528, 65.592
Angle α, β, γ (deg.)90.00, 100.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE II


Mass: 23345.139 Da / Num. of mol.: 2 / Fragment: AA9, RESIDUES 17-243
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN OF NCLPMO9C
Source: (gene. exp.) NEUROSPORA CRASSA (STRAIN ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: GH61-3, NCU02916 / Plasmid: PPINK-GAPHC / Production host: PICHIA PASTORIS (fungus) / Strain (production host): PICHIAPINK STRAIN4 / References: UniProt: Q7SHI8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCATALYTIC DOMAIN OF FULL LENGTH ENZYME

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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: 1.93 Å3/Da / Density % sol: 36.4 % / Description: NONE
Crystal growpH: 8 / Details: 0.2M ZINC ACETATE, 17.5% PEG3350, pH 8

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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: Dec 15, 2013 / 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: 1.9→64.41 Å / Num. obs: 29831 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAME PROTEIN WITH ONE METAL INSTEAD OF 3

Resolution: 1.9→64.406 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.829 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 182-184 HAVE BEEN OMITTED IN CHAINB DUE TO INSUFFICIENT ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1510 5.15 %RANDOM
Rwork0.2122 ---
obs0.215 29810 99.135 %-
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: 9.993 Å2
Baniso -1Baniso -2Baniso -3
1--1.727 Å20 Å20.116 Å2
2--2.533 Å20 Å2
3----0.792 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 50 423 3732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193472
X-RAY DIFFRACTIONr_bond_other_d0.0010.023220
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9394733
X-RAY DIFFRACTIONr_angle_other_deg0.8063.0017424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695.021475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07325.878131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42715498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.193154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
X-RAY DIFFRACTIONr_nbd_refined0.270.21123
X-RAY DIFFRACTIONr_nbd_other0.2220.290
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21719
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.23
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_it0.7020.9611865
X-RAY DIFFRACTIONr_mcbond_other0.6990.9571856
X-RAY DIFFRACTIONr_mcangle_it1.2491.4312335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7540.951607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1761.4092395
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 107 -
Rwork0.308 2086 -
obs--98.253 %

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