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- PDB-3si2: Structure of glycosylated murine glutaminyl cyclase in presence o... -

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Basic information

Entry
Database: PDB / ID: 3si2
TitleStructure of glycosylated murine glutaminyl cyclase in presence of the inhibitor PQ50 (PDBD150)
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha/beta hydrolase / Alzheimer's disease / pyroglutamate / pGlu / pE / pGlu-amyloid / glycosylation / glycoprotein / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Neutrophil degranulation / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / ACETATE ION / Chem-PBD / Glutaminyl-peptide cyclotransferase / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsParthier, C. / Carrillo, D. / Stubbs, M.T.
CitationJournal: Biochemistry / Year: 2011
Title: Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center.
Authors: Ruiz-Carrillo, D. / Koch, B. / Parthier, C. / Wermann, M. / Dambe, T. / Buchholz, M. / Ludwig, H.H. / Heiser, U. / Rahfeld, J.U. / Stubbs, M.T. / Schilling, S. / Demuth, H.U.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Aug 31, 2011Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7466
Polymers37,5771
Non-polymers1,1695
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.760, 83.060, 95.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glutaminyl-peptide cyclotransferase / / Glutaminyl cyclase / QC / Glutaminyl-tRNA cyclotransferase


Mass: 37577.477 Da / Num. of mol.: 1 / Fragment: UNP residues 36-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qpct / Plasmid: pPICZalphaB / Production host: Pichia pastoris (fungus) / Strain (production host): X33
References: UniProt: B2RX76, UniProt: Q9CYK2*PLUS, glutaminyl-peptide cyclotransferase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 346 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PBD / 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea


Mass: 320.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N4O2S
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 100 mM sodium acetate, 200 mM ammonium sulfate, 12% w/v PEG2000 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2008
RadiationMonochromator: BL 14.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 31637 / Num. obs: 31576 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 25.495 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.90.8192.3326654467999.9
1.9-20.5213.5821529374399.9
2-2.10.375.1176603092100
2.1-2.20.2786.5314778258399.9
2.2-2.660.15611.12426857457100
2.66-3.120.07819.71213803739100
3.12-3.580.05327.31117862088100
3.58-4.040.04332.916990125099.8
4.04-4.50.03536.354426796100
4.5-100.03436.9105961965100
10-200.02537.480418493.4
20-30
30

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.01 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.89 Å
Translation2.5 Å29.89 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.1phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SI1

3si1


Resolution: 1.8→19.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.347 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1579 5 %RANDOM
Rwork0.1844 ---
all0.1881 31574 --
obs0.1881 31574 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: 80.06 Å2 / Biso mean: 21.3925 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 74 342 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212775
X-RAY DIFFRACTIONr_angle_refined_deg2.2241.9723773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69523.796137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4861517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212137
X-RAY DIFFRACTIONr_mcbond_it1.2141.51620
X-RAY DIFFRACTIONr_mcangle_it2.01122613
X-RAY DIFFRACTIONr_scbond_it3.34431155
X-RAY DIFFRACTIONr_scangle_it4.9154.51157
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 114 -
Rwork0.285 2146 -
all-2260 -
obs--100 %

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