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- PDB-7d8e: Crystal Structure of double mutant Y115E Y117E human Secretory Gl... -

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Basic information

Entry
Database: PDB / ID: 7d8e
TitleCrystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09
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
Chem-GYO / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: To Be Published
Title: Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09
Authors: Dileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)114,81725
Polymers112,4683
Non-polymers2,34922
Water6,161342
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,39810
Polymers37,4891
Non-polymers9099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2408
Polymers37,4891
Non-polymers7517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1787
Polymers37,4891
Non-polymers6896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.181, 149.303, 94.539
Angle α, β, γ (deg.)90.000, 97.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1121-

HOH

21A-1215-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 37489.277 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E
Source method: isolated from a genetically manipulated source
Details: Cpd-09 / Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 5 types, 364 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GYO / ~{N}-[(1~{S},2~{S})-2-(2-methoxyphenyl)cyclopropyl]-3~{H}-benzimidazole-5-carboxamide


Mass: 307.346 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H17N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.34 % / Description: Hexagonal plate like crystals
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES buffer pH 6.0-6.5, 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: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.85 Å / Num. obs: 79687 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.9 / Num. measured all: 611144 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2-2.047.60.5173450245160.9254.5100
10.2-46.857.40.05346376290.99728.899.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWY

4ywy


Resolution: 2→46.85 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 4097 5.14 %
Rwork0.2087 75577 -
obs0.2109 79674 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.86 Å2 / Biso mean: 18.19 Å2 / Biso min: 4.25 Å2
Refinement stepCycle: final / Resolution: 2→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7590 0 143 342 8075
Biso mean--30.59 22.34 -
Num. residues----954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0198248
X-RAY DIFFRACTIONf_angle_d1.23711259
X-RAY DIFFRACTIONf_chiral_restr0.0781191
X-RAY DIFFRACTIONf_plane_restr0.0061464
X-RAY DIFFRACTIONf_dihedral_angle_d13.0293015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.02350.28831540.2242555
2.0235-2.04820.30311400.21612604
2.0482-2.07420.26061070.22112615
2.0742-2.10140.28811490.21272648
2.1014-2.13020.25731300.20362603
2.1302-2.16070.24051300.20152601
2.1607-2.19290.28861380.21072574
2.1929-2.22720.26021250.19872608
2.2272-2.26370.26021270.1952650
2.2637-2.30270.24751470.19772574
2.3027-2.34460.24781240.1982608
2.3446-2.38970.25491200.20432636
2.3897-2.43850.27721400.20472590
2.4385-2.49150.24371460.21042607
2.4915-2.54940.24811520.19612581
2.5494-2.61320.2471530.2092628
2.6132-2.68380.2421360.21912596
2.6838-2.76280.2741340.21882599
2.7628-2.8520.28781520.21572600
2.852-2.95390.27251370.21482618
2.9539-3.07210.27841300.22862616
3.0721-3.21190.26891340.2232620
3.2119-3.38120.23971660.22212559
3.3812-3.5930.25411580.21462605
3.593-3.87030.25822000.2062561
3.8703-4.25950.21361500.19642611
4.2595-4.87530.21621350.18282610
4.8753-6.14020.2831070.20892678
6.1402-46.850.20861760.20862622

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