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- PDB-7cp0: Crystal Structure of double mutant Y115E Y117E human Secretory Gl... -

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Basic information

Entry
Database: PDB / ID: 7cp0
TitleCrystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Glutaminyl-peptide cyclotransferase / sQC / Alzheimer's disease / Pyroglutamate
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
Similarity search - Domain/homology
Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16F16385 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors.
Authors: Dileep, K.V. / Sakai, N. / Ihara, K. / Kato-Murayama, M. / Nakata, A. / Ito, A. / Sivaraman, D.M. / Shin, J.W. / Yoshida, M. / Shirouzu, M. / Zhang, K.Y.J.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,78130
Polymers111,9933
Non-polymers1,78827
Water11,674648
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,98911
Polymers37,3311
Non-polymers65810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,92710
Polymers37,3311
Non-polymers5969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8659
Polymers37,3311
Non-polymers5348
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.277, 149.383, 96.032
Angle α, β, γ (deg.)90.000, 96.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-526-

HOH

21C-695-

HOH

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Components

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


Mass: 37331.121 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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 / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: Hexagonal plate like crystals
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES buffer pH 6.5, 46-67 mM NaOH, 100 mM ammonium sulfate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.05 Å / Num. obs: 131782 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6 / Num. measured all: 494444 / Scaling rejects: 151
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.7-1.733.70.532460965710.8042.899.9
9.31-43.053.60.04330088250.99625.998.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWY

4ywy


Resolution: 1.7→43.05 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 6642 5 %RANDOM
Rwork0.2054 ---
obs0.2063 125101 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.93 Å2 / Biso mean: 17.651 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 102 648 8576
Biso mean--23.1 21.57 -
Num. residues----981
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 500 -
Rwork0.244 9236 -
all-9736 -
obs--99.93 %

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