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- PDB-4qi8: Lytic polysaccharide monooxygenase 9F from Neurospora crassa, NcLPMO9F -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4qi8
TitleLytic polysaccharide monooxygenase 9F from Neurospora crassa, NcLPMO9F
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / beta-sandwich / cellulose degradation / electron transfer / cellulose / cellobiose dehydrogenase
Function / homology
Function and homology information


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
COPPER (II) ION / NITRATE ION / Endoglucanase II / Lytic polysaccharide monooxygenase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsTan, T.C. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Ludwig, R. / Hallberg, B.M. / Divne, C.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.
Authors: Tan, T.C. / Kracher, D. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Hallberg, B.M. / Ludwig, R. / Divne, C.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 7, 2018Group: 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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6275
Polymers46,4372
Non-polymers1893
Water15,097838
1
A: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3443
Polymers23,2191
Non-polymers1262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2822
Polymers23,2191
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 162.490, 32.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Lytic polysaccharide monooxygenase


Mass: 23218.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Strain: OR74A / Gene: B10C3.010, gh61-6, ncu03328 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q873G1, UniProt: Q1K4Q1*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium nitrate, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→43.22 Å / Num. all: 151544 / Num. obs: 151544 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→43.22 Å / SU ML: 0.06 / σ(F): 1.99 / Phase error: 13.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1491 1999 1.32 %RANDOM
Rwork0.1311 ---
obs0.1313 151531 96.21 %-
all-151531 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 6 838 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073518
X-RAY DIFFRACTIONf_angle_d1.2524844
X-RAY DIFFRACTIONf_dihedral_angle_d12.3221247
X-RAY DIFFRACTIONf_chiral_restr0.075515
X-RAY DIFFRACTIONf_plane_restr0.008636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12750.20991000.15087562X-RAY DIFFRACTION69
1.1275-1.1580.13821200.11888968X-RAY DIFFRACTION82
1.158-1.19210.12531420.110210586X-RAY DIFFRACTION96
1.1921-1.23060.14251460.119910976X-RAY DIFFRACTION100
1.2306-1.27450.14551480.115611013X-RAY DIFFRACTION100
1.2745-1.32560.14941470.125510955X-RAY DIFFRACTION99
1.3256-1.38590.15881470.11511008X-RAY DIFFRACTION100
1.3859-1.4590.15321470.114711034X-RAY DIFFRACTION100
1.459-1.55040.14981480.113811064X-RAY DIFFRACTION100
1.5504-1.67010.13981480.111511084X-RAY DIFFRACTION100
1.6701-1.83820.12811490.119611169X-RAY DIFFRACTION100
1.8382-2.10420.12721500.129111116X-RAY DIFFRACTION100
2.1042-2.6510.15711510.142911281X-RAY DIFFRACTION100
2.651-43.2580.16271560.150811716X-RAY DIFFRACTION100

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