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- PDB-5nru: Cys-Gly dipeptidase GliJ in complex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 5nru
TitleCys-Gly dipeptidase GliJ in complex with Zn2+
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
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
Hans-Fischer-Gesellschaft Germany
SFB749 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 23, 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 gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1744
Polymers45,0081
Non-polymers1663
Water3,153175
1
A: Dipeptidase gliJ
hetero molecules

A: Dipeptidase gliJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3498
Polymers90,0162
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area7120 Å2
ΔGint-217 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.210, 99.210, 106.670
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
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: 1.28096 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: 1.28096 Å / Relative weight: 1
ReflectionResolution: 2.15→45 Å / Num. obs: 63700 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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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: 2.15→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.743 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21076 1666 5 %RANDOM
Rwork0.19405 ---
obs0.19487 31661 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.581 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 3 175 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193071
X-RAY DIFFRACTIONr_bond_other_d0.0010.022868
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9534153
X-RAY DIFFRACTIONr_angle_other_deg0.88936616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79223.117154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8315535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3491533
X-RAY DIFFRACTIONr_chiral_restr0.0550.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023445
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_it0.8974.6861527
X-RAY DIFFRACTIONr_mcbond_other0.8974.6831526
X-RAY DIFFRACTIONr_mcangle_it0.8827.0231907
X-RAY DIFFRACTIONr_mcangle_other0.8827.0261908
X-RAY DIFFRACTIONr_scbond_it1.275.111544
X-RAY DIFFRACTIONr_scbond_other1.275.1111545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.117.4982247
X-RAY DIFFRACTIONr_long_range_B_refined2.02355.5183344
X-RAY DIFFRACTIONr_long_range_B_other1.86255.2523319
X-RAY DIFFRACTIONr_rigid_bond_restr1.07835937
X-RAY DIFFRACTIONr_sphericity_free26.5435115
X-RAY DIFFRACTIONr_sphericity_bonded5.21955952
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 120 -
Rwork0.29 2276 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -14.078 Å / Origin y: 68.7041 Å / Origin z: 16.7057 Å
111213212223313233
T0.0569 Å2-0.0083 Å20.0026 Å2-0.0687 Å20.0056 Å2--0.0018 Å2
L0.0164 °20.0499 °2-0.0175 °2-0.3184 °20.0122 °2--0.0611 °2
S-0.0193 Å °0.008 Å °0.0019 Å °0.0051 Å °0.0266 Å °0.007 Å °0.027 Å °-0.0065 Å °-0.0073 Å °

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