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- PDB-7d17: Crystal structure of Macrostomum lignano glutaminyl cyclase -

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Basic information

Entry
Database: PDB / ID: 7d17
TitleCrystal structure of Macrostomum lignano glutaminyl cyclase
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN
Function / homologyglutaminyl-peptide cyclotransferase / Glutaminyl-peptide cyclotransferase-like / glutaminyl-peptide cyclotransferase activity / Peptidase M28 / Peptidase family M28 / metal ion binding / glutaminyl-peptide cyclotransferase
Function and homology information
Biological speciesMacrostomum lignano (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.998 Å
AuthorsHuang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-ITAR-11 Taiwan
Ministry of Science and Technology (MoST, Taiwan)AS-SUMMIT-109
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-TPP2
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-TSPA
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 14, 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 13, 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)37,4712
Polymers37,4051
Non-polymers651
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area13170 Å2
Unit cell
Length a, b, c (Å)84.855, 71.671, 49.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

21A-622-

HOH

31A-646-

HOH

41A-650-

HOH

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Components

#1: Protein Glutaminyl-peptide cyclotransferase


Mass: 37405.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrostomum lignano (invertebrata) / Gene: BOX15_Mlig028993g1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A267GXB9, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium HEPES, pH 7.5, 70% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→30 Å / Num. obs: 6437 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 59.95 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 7.9
Reflection shellResolution: 2.998→3.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2 / Num. unique obs: 618 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHN

4mhn


Resolution: 2.998→29.466 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 303 5.01 %
Rwork0.187 5750 -
obs0.1893 6053 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.82 Å2 / Biso mean: 52.4904 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 2.998→29.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 1 153 2676
Biso mean--33.91 49.37 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.998-3.090.27411380.1818262287
3.7755-29.4660.21481650.1893312899

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