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- PDB-4yu9: Crystal Structure of double mutant Y115E Y117E human Glutaminyl C... -

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Basic information

Entry
Database: PDB / ID: 4yu9
TitleCrystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Alzheimer Disease / Drug Target
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / 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
Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDi Pisa, F. / Pozzi, C. / Benvenuti, M. / Mangani, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The soluble Y115E-Y117E variant of human glutaminyl cyclase is a valid target for X-ray and NMR screening of inhibitors against Alzheimer disease.
Authors: DiPisa, F. / Pozzi, C. / Benvenuti, M. / Andreini, M. / Marconi, G. / Mangani, S.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,88324
Polymers112,4683
Non-polymers1,41521
Water16,916939
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,11910
Polymers37,4891
Non-polymers6309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8657
Polymers37,4891
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8997
Polymers37,4891
Non-polymers4106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.380, 149.630, 96.300
Angle α, β, γ (deg.)90.00, 96.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-501-

HOH

21C-552-

HOH

31C-561-

HOH

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Components

#1: Protein Glutaminyl-peptide cyclotransferase / Glutaminyl cyclase / sQC / Glutaminyl-tRNA cyclotransferase / Glutamyl cyclase / EC


Mass: 37489.277 Da / Num. of mol.: 3 / Fragment: UNP residues 33-361 / Mutation: Y115E, Y117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→95.7 Å / Num. obs: 66975 / % possible obs: 95 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→95.65 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.8 / SU B: 5.22 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 3350 5.1 %RANDOM
Rwork0.21079 ---
obs0.213 62069 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.992 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→95.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7721 0 78 939 8738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198034
X-RAY DIFFRACTIONr_bond_other_d0.0020.027513
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.96110916
X-RAY DIFFRACTIONr_angle_other_deg0.896317271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.867375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.411151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.611547
X-RAY DIFFRACTIONr_chiral_restr0.1020.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.2893907
X-RAY DIFFRACTIONr_mcbond_other1.1311.2883906
X-RAY DIFFRACTIONr_mcangle_it1.8671.9184872
X-RAY DIFFRACTIONr_mcangle_other1.8671.9184873
X-RAY DIFFRACTIONr_scbond_it1.531.4154127
X-RAY DIFFRACTIONr_scbond_other1.5291.4154127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4322.0616037
X-RAY DIFFRACTIONr_long_range_B_refined4.96111.210103
X-RAY DIFFRACTIONr_long_range_B_other4.6910.8449714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 253 -
Rwork0.215 4734 -
obs--95.76 %

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