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- PDB-5lx4: Cys-Gly dipeptidase GliJ mutant D38H -

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Basic information

Entry
Database: PDB / ID: 5lx4
TitleCys-Gly dipeptidase GliJ mutant D38H
ComponentsDipeptidase
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 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
Hans-Fischer-Gesellschaft 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
DepositionSep 20, 2016Deposition 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 1.2Dec 19, 2018Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_conn_angle ...pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4556
Polymers45,0311
Non-polymers4245
Water5,188288
1
A: Dipeptidase
hetero molecules

A: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,91112
Polymers90,0622
Non-polymers84810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7320 Å2
ΔGint-62 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.970, 98.970, 106.050
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


Mass: 45031.121 Da / Num. of mol.: 1 / Mutation: D38H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: AFUA_6G09650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WMJ8, membrane dipeptidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
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: 3.33 Å3/Da / Density % sol: 63.06 %
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 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 46949 / % possible obs: 98.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LX0

5lx0


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.457 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19027 2342 5 %RANDOM
Rwork0.16321 ---
obs0.16455 44493 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å2-0 Å2
2--0.17 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 25 288 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193123
X-RAY DIFFRACTIONr_bond_other_d0.0020.023023
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9574225
X-RAY DIFFRACTIONr_angle_other_deg0.9193.0016920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81123.013156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53515545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1161534
X-RAY DIFFRACTIONr_chiral_restr0.0640.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
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_it1.1933.6421538
X-RAY DIFFRACTIONr_mcbond_other1.1923.6411537
X-RAY DIFFRACTIONr_mcangle_it1.4955.4541925
X-RAY DIFFRACTIONr_mcangle_other1.4965.4561926
X-RAY DIFFRACTIONr_scbond_it1.6434.011585
X-RAY DIFFRACTIONr_scbond_other1.6434.011585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8455.8842296
X-RAY DIFFRACTIONr_long_range_B_refined3.09929.5253662
X-RAY DIFFRACTIONr_long_range_B_other3.09829.5283663
X-RAY DIFFRACTIONr_rigid_bond_restr0.73936144
X-RAY DIFFRACTIONr_sphericity_free34.026596
X-RAY DIFFRACTIONr_sphericity_bonded9.12356280
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 172 -
Rwork0.228 3264 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -35.3562 Å / Origin y: 17.1496 Å / Origin z: 16.5988 Å
111213212223313233
T0.0243 Å2-0.0043 Å2-0.0007 Å2-0.0302 Å2-0.0015 Å2--0.0006 Å2
L0.008 °2-0.0172 °2-0.0068 °2-0.074 °20.0003 °2--0.0158 °2
S-0.0022 Å °0.0003 Å °0.0009 Å °0.0018 Å °0.0017 Å °-0.0059 Å °-0.0066 Å °0.0064 Å °0.0005 Å °

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