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- PDB-2afx: Crystal structure of human glutaminyl cyclase in complex with 1-b... -

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Basic information

Entry
Database: PDB / ID: 2afx
TitleCrystal structure of human glutaminyl cyclase in complex with 1-benzylimidazole
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / alpha-beta protein / metalloprotein
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 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-BENZYL-1H-IMIDAZOLE / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsHuang, K.F. / Liu, Y.L. / Cheng, W.J. / Ko, T.P. / Wang, A.H.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation
Authors: Huang, K.F. / Liu, Y.L. / Cheng, W.J. / Ko, T.P. / Wang, A.H.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7548
Polymers75,1152
Non-polymers6396
Water10,647591
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8774
Polymers37,5571
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8774
Polymers37,5571
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
hetero molecules

A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
hetero molecules

A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,26224
Polymers225,3446
Non-polymers1,91818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18230 Å2
ΔGint-390 kcal/mol
Surface area67160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.013, 119.013, 332.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

21A-711-

HOH

31B-695-

HOH

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Components

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


Mass: 37557.398 Da / Num. of mol.: 2 / Fragment: residues 33-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1BN / 1-BENZYL-1H-IMIDAZOLE / 1-BENZYLIMIDAZOLE


Mass: 158.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, dioxane, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11231
21231
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.975
SYNCHROTRONPhoton Factory BL-5A20.9792, 0.9794, 0.9750
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 13, 2004
ADSC QUANTUM 42CCDJun 13, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9751
20.97921
30.97941
ReflectionResolution: 1.64→50 Å / Num. all: 111111 / Num. obs: 100111 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.2
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.6 / % possible all: 93.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.64→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.205 4834 RANDOM
Rwork0.177 --
all0.186 95889 -
obs0.186 91055 -
Refinement stepCycle: LAST / Resolution: 1.64→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 36 591 5847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.87

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