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- PDB-4mhz: Crystal structure of apo-form glutaminyl cyclase from Ixodes scap... -

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Basic information

Entry
Database: PDB / ID: 4mhz
TitleCrystal structure of apo-form glutaminyl cyclase from Ixodes scapularis in complex with PBD150
ComponentsGlutaminyl cyclase, putative
KeywordsTRANSFERASE / alpha/beta-mixed fold / glutaminyl cyclase / PBD150 / secreted protein
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / 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 speciesIxodes scapularis (black-legged tick)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHuang, K.F. / Hsu, H.L. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding.
Authors: Huang, K.F. / Hsu, H.L. / Karim, S. / Wang, A.H.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Nov 8, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminyl cyclase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1292
Polymers37,8091
Non-polymers3201
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.259, 71.435, 80.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutaminyl cyclase, putative


Mass: 37808.660 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP RESIDUES 28-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Gene: IscW_ISCW023264 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL
References: UniProt: B7QK46, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-PBD / 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea


Mass: 320.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% (w/v) PEG 8000, 8% (v/v) ethylene glycol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 4, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 23824 / Num. obs: 21418 / % possible obs: 89.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2102 / % possible all: 90.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AFM

2afm


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.795 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22133 843 5.1 %RANDOM
Rwork0.1664 ---
all0.17 22522 --
obs0.16936 15718 69.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 22 261 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022746
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9573720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04123.151146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74515461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2071527
X-RAY DIFFRACTIONr_chiral_restr0.1030.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212139
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 1 -
Rwork0.106 93 -
obs--5.48 %

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