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- PDB-9ce9: Solution NMR structure of the fungal loosenin PcaLOOL12 from Phan... -

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Basic information

Entry
Database: PDB / ID: 9ce9
TitleSolution NMR structure of the fungal loosenin PcaLOOL12 from Phanerochaete carnosa
ComponentsRlpA-like protein double-psi beta-barrel domain-containing protein
KeywordsSUGAR BINDING PROTEIN / Expansin / Non-lytic / Cellulose / Carbohydrate-active enzymes / Defibrillation
Function / homologyRlpA-like domain superfamily / RlpA-like protein double-psi beta-barrel domain-containing protein
Function and homology information
Biological speciesPhanerochaete carnosa
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Master, E.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC05-76RL01830 United States
CitationJournal: To Be Published
Title: Bio-SANS investigation of fungal loosenins reveal substrate dependent impacts of protein action on inter-fibril distance and packing order of cellulosic substrates
Authors: Buchko, G.W. / Master, E.R.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RlpA-like protein double-psi beta-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)10,7801
Polymers10,7801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, The retention time on a gel filtration column and estimated rotational correlation time (tc) were consistent with a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein RlpA-like protein double-psi beta-barrel domain-containing protein


Mass: 10779.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete carnosa (strain HHB-10118-sp) (fungus)
Strain: HHB-10118-sp / Gene: PHACADRAFT_262410 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5VZD3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
1101isotropic13D HNCO
191isotropic13D HNCA
181isotropic13D CBCA(CO)NH
171isotropic13D HN(CA)CB
161isotropic13D C(CO)NH
1112isotropic12D 1H-13C HSQC aliphatic
1123isotropic1Deuterium exchange
1131isotropic13D 1H-15N TOCSY
1141isotropic12D 1H-13C HSQC aromatic
1151isotropic13D HN(CA)CO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] PcaLOOL12, 100 mM sodium chloride, 20 mM TRIS, 93% H2O/7% D2OPcaLOOL1293% H2O/7% D2O
solution20.8 mM [U-10% 13C; U-99% 15N] PcaLOOL12, 100 mM sodium chloride, 20 mM TRIS, 93% H2O/7% D2OPcaLOOL1293% H2O/7% D2O
solution30.4 mM [U-99% 15N] PcaLOOL12, 100 mM sodium chloride, 20 mM TRIS, 93% H2O/7% D2OPcaLOOL1293% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPcaLOOL12[U-99% 13C; U-99% 15N]1
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
0.8 mMPcaLOOL12[U-10% 13C; U-99% 15N]2
100 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance2
0.4 mMPcaLOOL12[U-99% 15N]3
100 mMsodium chloridenatural abundance3
20 mMTRISnatural abundance3
Sample conditionsIonic strength: 0.12 mM / Ionic strength err: 0.005 / Label: all / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
CYANA1.2Guntert, Mumenthaler and Wuthrichstructure calculation
CNSSOLVE1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOS+Shen, Delaglio, Cornilescu and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 10% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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