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- PDB-7d2b: Crystal structure of Ixodes scapularis glutaminyl cyclase with a ... -

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Basic information

Entry
Database: PDB / ID: 7d2b
TitleCrystal structure of Ixodes scapularis glutaminyl cyclase with a Ni ion bound to the active site
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
NICKEL (II) ION / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesIxodes scapularis (black-legged tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsHuang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-ITAR-11, AS-SUMMIT-109, AS-KPQ-109-TPP2, AS-KPQ-109-TSPA Taiwan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes.
Authors: Huang, K.F. / Huang, J.S. / Wu, M.L. / Hsieh, W.L. / Hsu, K.C. / Hsu, H.L. / Ko, T.P. / Wang, A.H.
History
DepositionSep 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3072
Polymers38,2481
Non-polymers591
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area14790 Å2
Unit cell
Length a, b, c (Å)55.066, 71.260, 80.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutaminyl-peptide cyclotransferase


Mass: 38248.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Gene: 8042451, IscW_ISCW023264 / Production host: Escherichia coli (E. coli)
References: UniProt: B7QK46, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293.15 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2017
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 21061 / % possible obs: 95.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2 / Num. unique obs: 2046 / % possible all: 94.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHN

4mhn


Resolution: 1.99→22.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.702 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1072 5.1 %RANDOM
Rwork0.1718 ---
obs0.1746 19960 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.08 Å2 / Biso mean: 30.412 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 1.99→22.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 1 245 2911
Biso mean--31.61 38.63 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192733
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9483706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51623.197147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67615463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571527
X-RAY DIFFRACTIONr_chiral_restr0.0990.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212130
LS refinement shellResolution: 1.992→2.044 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 79 -
Rwork0.238 1327 -
all-1406 -
obs--86.58 %

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