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- PDB-8hy3: Crystal structure of human secretory glutaminyl cyclase in comple... -

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Basic information

Entry
Database: PDB / ID: 8hy3
TitleCrystal structure of human secretory glutaminyl cyclase in complex with 1-benzyl-5-methyl-1H-imidazole
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / inhibitor / complex
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
: / CARBON DIOXIDE / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsLi, G.-B. / Deng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065;82073698;81874291 China
CitationJournal: To Be Published
Title: Crystal structure of human secretory glutaminyl cyclase in complex with 1-benzyl-5-methyl-1H-imidazole
Authors: Li, G.-B. / Deng, J.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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)37,9315
Polymers37,5571
Non-polymers3744
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-2 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.952, 273.952, 273.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37557.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 5 types, 46 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4Q8 / 5-methyl-1-(phenylmethyl)imidazole


Mass: 172.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 5.7 Å3/Da / Density % sol: 78.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 14%-18% (v/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 198 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→20.03 Å / Num. obs: 64779 / % possible obs: 99.79 % / Redundancy: 76.1 % / Rmerge(I) obs: 0.448 / Rpim(I) all: 0.051 / Rrim(I) all: 0.451 / Net I/σ(I): 10.9
Reflection shellResolution: 1.94→2.01 Å / Num. unique obs: 6251 / CC1/2: 0.009

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Processing

Software
NameVersionClassification
PHENIX1.95188-19.6181refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.952→19.618 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 42.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1998 3.8 %
Rwork0.2264 --
obs0.2276 52532 82.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→19.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 23 42 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172713
X-RAY DIFFRACTIONf_angle_d1.2273682
X-RAY DIFFRACTIONf_dihedral_angle_d15.2241599
X-RAY DIFFRACTIONf_chiral_restr0.06391
X-RAY DIFFRACTIONf_plane_restr0.008479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.952-2.00060.4327570.39211447X-RAY DIFFRACTION33
2.0006-2.05470.39691370.38243439X-RAY DIFFRACTION80
2.0547-2.11510.45781250.41323159X-RAY DIFFRACTION74
2.1151-2.18330.43941540.41923958X-RAY DIFFRACTION91
2.1833-2.26120.39251550.38713912X-RAY DIFFRACTION91
2.2612-2.35160.38761550.33253899X-RAY DIFFRACTION90
2.3516-2.45840.31471550.30693913X-RAY DIFFRACTION90
2.4584-2.58770.311550.30883921X-RAY DIFFRACTION90
2.5877-2.74950.34241550.28123905X-RAY DIFFRACTION89
2.7495-2.96110.3351530.25863898X-RAY DIFFRACTION89
2.9611-3.25790.2891540.24733878X-RAY DIFFRACTION88
3.2579-3.72650.26481510.21983837X-RAY DIFFRACTION86
3.7265-4.68440.20451500.18133779X-RAY DIFFRACTION84
4.6844-19.6180.18711420.17463589X-RAY DIFFRACTION76

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