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- PDB-7d18: Crystal structure of Acidobacteriales bacterium glutaminyl cyclase -

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Basic information

Entry
Database: PDB / ID: 7d18
TitleCrystal structure of Acidobacteriales bacterium glutaminyl cyclase
ComponentsPeptidase M28
KeywordsTRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN
Function / homologyGlutaminyl-peptide cyclotransferase-like / glutaminyl-peptide cyclotransferase activity / Peptidase M28 / Peptidase family M28 / zinc ion binding / Peptidase M28
Function and homology information
Biological speciesAcidobacteriales bacterium 59-55 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.332 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 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase M28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,90816
Polymers32,5651
Non-polymers1,34315
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-114 kcal/mol
Surface area12770 Å2
Unit cell
Length a, b, c (Å)37.044, 78.330, 44.892
Angle α, β, γ (deg.)90.000, 111.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidase M28


Mass: 32564.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacteriales bacterium 59-55 (bacteria)
Gene: BGO25_06485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q3QTC5

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Non-polymers , 6 types, 346 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 31.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.5, 30% (w/v) PEG 8000

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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: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→30 Å / Num. obs: 53659 / % possible obs: 98.5 % / Redundancy: 10 % / Biso Wilson estimate: 13.73 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 28
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 5037 / % possible all: 92.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
ARP/wARPmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.332→25.909 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1403 2003 3.74 %
Rwork0.1141 51486 -
obs0.1151 53489 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.04 Å2 / Biso mean: 18.5238 Å2 / Biso min: 9.5 Å2
Refinement stepCycle: final / Resolution: 1.332→25.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 80 331 2710
Biso mean--35.2 33.45 -
Num. residues----293
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3323-1.36560.18021240.1305321386
1.3656-1.40250.19221510.125363798
1.4025-1.44380.1711400.1168365398
1.4438-1.49040.15171440.099368198
1.4904-1.54360.12721330.0878369698
1.5436-1.60540.1391510.0826369699
1.6054-1.67850.10971480.0822366999
1.6785-1.7670.12411400.0898374599
1.767-1.87770.15541420.0945370599
1.8777-2.02260.12521520.09323712100
2.0226-2.2260.12831410.10113749100
2.226-2.54790.15581400.11833762100
2.5479-3.20910.16181500.1293765100
3.2091-25.9090.12481470.12483803100

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