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- PDB-2zem: Crystal structure of the human glutaminyl cyclase mutant D248Q at... -

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Basic information

Entry
Database: PDB / ID: 2zem
TitleCrystal structure of the human glutaminyl cyclase mutant D248Q at 2.18 angstrom resolution
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / hydrogen bond network / glutaminyl cyclase / pyroglutamate / site-directed mutagenesis / proton transfer / Acyltransferase / Glycoprotein / Metal-binding
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 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsHuang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / Wang, A.H.
CitationJournal: Biochem.J. / Year: 2008
Title: A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis.
Authors: Huang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / Wang, A.H.
History
DepositionDec 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,4646
Polymers75,1412
Non-polymers3234
Water11,349630
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7323
Polymers37,5701
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7323
Polymers37,5701
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
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)226,39118
Polymers225,4236
Non-polymers96912
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 area14940 Å2
ΔGint-436 kcal/mol
Surface area68360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.778, 118.778, 332.500
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-684-

HOH

21B-753-

HOH

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Components

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


Mass: 37570.438 Da / Num. of mol.: 2 / Fragment: residues 33-361 / Mutation: D248Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: bone marow / Gene: QPCT / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2%-4% dioxane, 1.6-1.8M ammonium sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 47679 / Num. obs: 46201 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 23.1
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4519 / Rsym value: 0.597 / % possible all: 95.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2AFM

2afm


Resolution: 2.18→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2114 -RANDOM
Rwork0.179 ---
all0.1812 47536 --
obs0.18 42632 95.9 %-
Displacement parametersBiso mean: 37.8 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 12 630 5856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.18→2.26 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.267 199 -
Rwork0.223 --
obs-4054 89.7 %

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