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- PDB-4fbe: Crystal structure of the C136A/C164A variant of mitochondrial iso... -

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Basic information

Entry
Database: PDB / ID: 4fbe
TitleCrystal structure of the C136A/C164A variant of mitochondrial isoform of glutaminyl cyclase from Drosophila melanogaster
ComponentsCG5976, isoform B
KeywordsTRANSFERASE / HYDROLASE / alpha/beta hydrolase / pGlu formation / PE / Alzheimer's Disease / pyroglutamate / pGlu-amyloid
Function / homology
Function and homology information


glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Neutrophil degranulation / mitochondrion / extracellular region / zinc ion binding
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
Chem-PBD / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKolenko, P. / Koch, B. / Ruiz-Carilo, D. / Stubbs, M.T.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structures of Glutaminyl Cyclases (QCs) from Drosophila melanogaster Reveal Active Site Conservation between Insect and Mammalian QCs.
Authors: Koch, B. / Kolenko, P. / Buchholz, M. / Ruiz Carrillo, D. / Parthier, C. / Wermann, M. / Rahfeld, J.U. / Reuter, G. / Schilling, S. / Stubbs, M.T. / Demuth, H.U.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG5976, isoform B
B: CG5976, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5397
Polymers75,7322
Non-polymers8075
Water7,638424
1
A: CG5976, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2874
Polymers37,8661
Non-polymers4213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CG5976, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2523
Polymers37,8661
Non-polymers3862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.928, 46.436, 74.150
Angle α, β, γ (deg.)84.93, 75.17, 74.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CG5976, isoform B / glutaminyl-peptide cyclotransferase / RE61650p


Mass: 37866.172 Da / Num. of mol.: 2 / Fragment: UNP residues 32-354 / Mutation: C136A, C164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: isoQC, CG5976, Dmel_CG5976 / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q86PD7, glutaminyl-peptide cyclotransferase, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-PBD / 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea


Mass: 320.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20N4O2S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2 M magnesium chloride, 1 mM PQ50, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 10, 2010 / Details: MIRRORS
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.88→71.663 Å / Num. all: 36766 / Num. obs: 36763 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.2
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1926 / % possible all: 28.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FAI

4fai


Resolution: 1.88→71.66 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 2.261 / SU ML: 0.071 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1837 -RANDOM
Rwork0.1705 ---
all0.17463 36763 --
obs0.17463 36763 79.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20.4 Å20.58 Å2
2--0.71 Å2-0.09 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.88→71.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 47 424 5401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225127
X-RAY DIFFRACTIONr_bond_other_d0.0020.023490
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9746966
X-RAY DIFFRACTIONr_angle_other_deg0.8993.0018465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9323.77244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95715871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8161531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.195 718 -
obs--20.78 %

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