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- PDB-5nry: Cys-Gly dipeptidase GliJ in complex with Fe3+ -

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Basic information

Entry
Database: PDB / ID: 5nry
TitleCys-Gly dipeptidase GliJ in complex with Fe3+
ComponentsDipeptidase gliJ
KeywordsHYDROLASE / carboxypeptidase / dipeptidase / gliotoxin biosynthesis
Function / homology
Function and homology information


symbiont-mediated suppression of host immune response / gliotoxin biosynthetic process / membrane dipeptidase / mycotoxin biosynthetic process / metallodipeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Dipeptidase gliJ
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
Hans-Fischer-Gesellschaft Germany
German Research FoundationSFB749 Germany
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ.
Authors: Marion, A. / Groll, M. / Scharf, D.H. / Scherlach, K. / Glaser, M. / Sievers, H. / Schuster, M. / Hertweck, C. / Brakhage, A.A. / Antes, I. / Huber, E.M.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidase gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2266
Polymers45,0081
Non-polymers2185
Water6,900383
1
A: Dipeptidase gliJ
hetero molecules

A: Dipeptidase gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45212
Polymers90,0162
Non-polymers43610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area7770 Å2
ΔGint-148 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.990, 98.990, 106.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dipeptidase gliJ / Gliotoxin biosynthesis protein J


Mass: 45008.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: gliJ, AFUA_6G09650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WMJ8, membrane dipeptidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 5% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.73842 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73842 Å / Relative weight: 1
ReflectionResolution: 1.85→45 Å / Num. obs: 98319 / % possible obs: 98.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.2
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.6 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LX0

5lx0


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.91 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18991 2560 5 %RANDOM
Rwork0.16488 ---
obs0.16612 48627 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å2-0 Å2
3----1.6 Å2
Refinement stepCycle: 1 / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 5 383 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193069
X-RAY DIFFRACTIONr_bond_other_d0.0010.022864
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9534152
X-RAY DIFFRACTIONr_angle_other_deg0.89636608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60623.161155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13215536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8851533
X-RAY DIFFRACTIONr_chiral_restr0.0570.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7363.5521525
X-RAY DIFFRACTIONr_mcbond_other0.7353.551524
X-RAY DIFFRACTIONr_mcangle_it0.8845.321905
X-RAY DIFFRACTIONr_mcangle_other0.8845.3221906
X-RAY DIFFRACTIONr_scbond_it1.0413.9221544
X-RAY DIFFRACTIONr_scbond_other1.0413.9231545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0175.7472247
X-RAY DIFFRACTIONr_long_range_B_refined2.17443.7443490
X-RAY DIFFRACTIONr_long_range_B_other1.77542.6373382
X-RAY DIFFRACTIONr_rigid_bond_restr0.54335931
X-RAY DIFFRACTIONr_sphericity_free21.3155223
X-RAY DIFFRACTIONr_sphericity_bonded7.19856041
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 167 -
Rwork0.271 3167 -
obs--89.03 %
Refinement TLS params.Method: refined / Origin x: -14.1482 Å / Origin y: 68.5875 Å / Origin z: 16.6323 Å
111213212223313233
T0.0142 Å2-0.0073 Å20.0012 Å2-0.0224 Å20.0052 Å2--0.0034 Å2
L0.0043 °20.0034 °20.0107 °2-0.1912 °2-0.0074 °2--0.0587 °2
S-0.0052 Å °0.0026 Å °-0.0019 Å °-0.0049 Å °0.0146 Å °0.0113 Å °0.0116 Å °-0.0079 Å °-0.0094 Å °

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