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- PDB-5u22: Structure of N2152 from Neocallimastix frontalis -

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Basic information

Entry
Database: PDB / ID: 5u22
TitleStructure of N2152 from Neocallimastix frontalis
ComponentsN2152
KeywordsHYDROLASE / Glycoside Hydrolase / TIM Barrel / Beta Sandwich
Function / homologyGlycosyl hydrolases family 39 / Glycoside hydrolase superfamily / IODIDE ION / N2152
Function and homology information
Biological speciesNeocallimastix frontalis (fungus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.748 Å
AuthorsJones, D.R. / Abbott, D.W.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl substrates.
Authors: Jones, D.R. / Uddin, M.S. / Gruninger, R.J. / Pham, T.T.M. / Thomas, D. / Boraston, A.B. / Briggs, J. / Pluvinage, B. / McAllister, T.A. / Forster, R.J. / Tsang, A. / Selinger, L.B. / Abbott, D.W.
History
DepositionNov 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N2152
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,50418
Polymers47,4591
Non-polymers2,04517
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint10 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.986, 104.793, 49.445
Angle α, β, γ (deg.)90.000, 110.060, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by gel filtration

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Components

#1: Protein N2152


Mass: 47459.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neocallimastix frontalis (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A247D6Y4*PLUS
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, Bis-Tris, Sodium Iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.748→30 Å / Num. obs: 35446 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 19.11 Å2 / Rmerge(I) obs: 0.104 / Net I/av σ(I): 12.291 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.75-1.783.10.3810.764198.8
1.78-1.812.80.3440.814197.2
1.81-1.852.70.3030.835197.8
1.85-1.892.90.2770.878198.2
1.89-1.933.20.2420.886199.3
1.93-1.973.50.2230.92199.7
1.97-2.023.70.2010.939199.7
2.02-2.0740.1840.94199.8
2.07-2.144.20.1620.959199.9
2.14-2.24.90.1530.9671100
2.2-2.285.10.1450.9751100
2.28-2.375.30.1280.9811100
2.37-2.485.50.1160.985199.9
2.48-2.615.80.1080.9871100
2.61-2.786.20.1010.9881100
2.78-2.996.60.0880.9911100
2.99-3.296.70.0810.9931100
3.29-3.776.90.0770.9921100
3.77-4.746.80.0810.9911100
4.74-3060.0980.986199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data collection
HKL-3000data scaling
SHELXphasing
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
SHELXDphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.748→28.955 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.06
RfactorNum. reflection% reflection
Rfree0.1942 1850 5.24 %
Rwork0.1556 --
obs0.1576 35312 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89 Å2 / Biso mean: 19.3544 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 1.748→28.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 39 314 3527
Biso mean--31.17 25.98 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063293
X-RAY DIFFRACTIONf_angle_d0.8614464
X-RAY DIFFRACTIONf_chiral_restr0.055459
X-RAY DIFFRACTIONf_plane_restr0.006582
X-RAY DIFFRACTIONf_dihedral_angle_d10.8581938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7479-1.79510.24911270.18822373250092
1.7951-1.84790.23181510.17982528267997
1.8479-1.90760.21391500.17612511266198
1.9076-1.97570.22071540.16642609276399
1.9757-2.05480.22491190.149326112730100
2.0548-2.14830.2071530.161325762729100
2.1483-2.26150.21431340.15525852719100
2.2615-2.40320.21241460.153325792725100
2.4032-2.58860.2191560.164426022758100
2.5886-2.84890.18331470.160226202767100
2.8489-3.26070.21571200.158726132733100
3.2607-4.10620.18871420.13926412783100
4.1062-28.9590.13961510.15112614276599

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