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- PDB-3pms: Recombinant peptide: N-glycanase F (PNGase F) -

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Basic information

Entry
Database: PDB / ID: 3pms
TitleRecombinant peptide: N-glycanase F (PNGase F)
ComponentsPeptide:N-glycosidase F
KeywordsHYDROLASE / Jelly Roll Fold / N-Glycanase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / hydrolase activity, acting on glycosyl bonds
Similarity search - Function
: / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Peptide:N-glycosidase F
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsFilitcheva, J. / Anderson, B.F. / Norris, G.E.
CitationJournal: To be Published
Title: Recombinant peptide:N-glycanase F (PNGase F)
Authors: Filitcheva, J. / Anderson, B.F. / Norris, G.E.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide:N-glycosidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52415
Polymers36,2921
Non-polymers1,23114
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.96, 90.56, 48.81
Angle α, β, γ (deg.)90.000, 112.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide:N-glycosidase F


Mass: 36292.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Strain: CDC 3552 / Gene: png / Plasmid: OPH6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9XBM8, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2009
RadiationMonochromator: Capillary optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.57→40.41 Å / Num. all: 43449 / Num. obs: 41972 / % possible obs: 96.6 % / Rmerge(I) obs: 0.057

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PGS

1pgs


Resolution: 1.57→34.02 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.281 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 2256 5.1 %RANDOM
Rwork0.151 ---
obs0.1524 41972 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.05 Å2 / Biso mean: 18.3064 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0.4 Å2
2---0.92 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 78 424 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021771
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9533585
X-RAY DIFFRACTIONr_angle_other_deg0.92734330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0124.696115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67715411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.833159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_mcbond_it1.6081.51581
X-RAY DIFFRACTIONr_mcbond_other0.5351.5639
X-RAY DIFFRACTIONr_mcangle_it2.47522569
X-RAY DIFFRACTIONr_scbond_it3.28231055
X-RAY DIFFRACTIONr_scangle_it5.0444.51008
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 143 -
Rwork0.218 2468 -
all-2611 -
obs--100 %

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