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- PDB-9fxh: Crystal structure of cobalt(II)-substituted double mutant Y115E Y... -

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Basic information

Entry
Database: PDB / ID: 9fxh
TitleCrystal structure of cobalt(II)-substituted double mutant Y115E Y117E human Glutaminyl Cyclase
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / human glutaminyl cyclase / acyltransferase / hQC / cobalt
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 / extracellular region / zinc ion binding
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: 2.3 Å
AuthorsTassone, G. / Pozzi, C. / Mangani, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Int J Mol Sci / Year: 2024
Title: Metal Ion Binding to Human Glutaminyl Cyclase: A Structural Perspective.
Authors: Tassone, G. / Pozzi, C. / Mangani, S.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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)117,24110
Polymers116,6843
Non-polymers5577
Water19,2761070
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0503
Polymers38,8951
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0503
Polymers38,8951
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1424
Polymers38,8951
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.185, 149.266, 96.007
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-719-

HOH

21C-763-

HOH

31C-817-

HOH

41C-835-

HOH

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Components

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


Mass: 38894.789 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: PLASMID / Details (production host): pQE-80L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1-0.2 M ammonium sulphate and 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2023
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.3→61.76 Å / Num. obs: 50664 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.112 / Rrim(I) all: 0.194 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4761 / CC1/2: 0.747 / Rpim(I) all: 0.452 / Rrim(I) all: 0.772 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.825 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25657 2540 5 %RANDOM
Rwork0.20453 ---
obs0.20716 48122 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.3→61.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 24 1070 8852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.62910874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88822.437435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.777151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8311548
X-RAY DIFFRACTIONr_chiral_restr0.1010.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026191
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0132.7963881
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1834.1794839
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2922.8854108
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.85538.40112923
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 182 -
Rwork0.319 3613 -
obs--97.03 %

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