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- PDB-7d1b: Crystal structure of Fimbriiglobus ruber glutaminyl cyclase -

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Basic information

Entry
Database: PDB / ID: 7d1b
TitleCrystal structure of Fimbriiglobus ruber glutaminyl cyclase
ComponentsLeucine aminopeptidase
KeywordsTRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN
Function / homologyGlutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / acyltransferase activity / aminopeptidase activity / metal ion binding / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Leucine aminopeptidase
Function and homology information
Biological speciesFimbriiglobus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 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: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,49513
Polymers37,5001
Non-polymers99512
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-34 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.206, 73.436, 87.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine aminopeptidase


Mass: 37500.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fimbriiglobus ruber (bacteria) / Gene: FRUB_06987 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A225DNX9

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Non-polymers , 5 types, 414 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) PEG 8000, 0.1 M Tris-HCl, pH 8.5, 0.1 M MgCl2, 20% (v/v) PEG 400

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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: 1.24→30 Å / Num. obs: 102036 / % possible obs: 97.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.32 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 41.8
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 9674 / % possible all: 93.6

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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: 1.24→25.967 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 9.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1254 2000 1.97 %
Rwork0.111 99720 -
obs0.1113 101720 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.81 Å2 / Biso mean: 20.005 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.24→25.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 58 404 2831
Biso mean--35.91 35.71 -
Num. residues----302
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2405-1.27150.15381300.1242647689
1.2715-1.30590.12041390.1049693196
1.3059-1.34430.12851400.0931700096
1.3443-1.38770.10761400.0903700597
1.3877-1.43730.1131420.0874702197
1.4373-1.49480.11221410.0792705797
1.4948-1.56290.10911430.0776710398
1.5629-1.64530.09371420.0801712198
1.6453-1.74830.12351440.084719298
1.7483-1.88330.10641450.0871719999
1.8833-2.07270.11451460.0942725899
2.0727-2.37250.11261460.1078734499
2.3725-2.98840.13731490.1273739099
2.9884-25.9670.14141530.1346762399

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