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- PDB-5lwz: Cys-Gly dipeptidase GliJ (space group C2) -

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Basic information

Entry
Database: PDB / ID: 5lwz
TitleCys-Gly dipeptidase GliJ (space group C2)
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 speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 19, 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 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidase
B: Dipeptidase
C: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,00416
Polymers135,0243
Non-polymers98013
Water7,656425
1
A: Dipeptidase
B: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,60810
Polymers90,0162
Non-polymers5928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-89 kcal/mol
Surface area27430 Å2
MethodPISA
2
C: Dipeptidase
hetero molecules

C: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,79212
Polymers90,0162
Non-polymers77610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area8290 Å2
ΔGint-91 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.800, 100.250, 106.640
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dipeptidase /


Mass: 45008.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Gene: AFUA_6G09650 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q4WMJ8, membrane dipeptidase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
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: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 103656 / % possible obs: 97.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITQ

1itq


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 9.261 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19721 5168 5 %RANDOM
Rwork0.16711 ---
obs0.1686 98193 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.04 Å2
2--1.34 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9035 0 48 425 9508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199249
X-RAY DIFFRACTIONr_bond_other_d0.0020.028933
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.95712499
X-RAY DIFFRACTIONr_angle_other_deg0.912320436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94623.089463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.859151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.66115100
X-RAY DIFFRACTIONr_chiral_restr0.0640.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022206
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_it1.4884.2994579
X-RAY DIFFRACTIONr_mcbond_other1.4864.2984578
X-RAY DIFFRACTIONr_mcangle_it1.9616.4395719
X-RAY DIFFRACTIONr_mcangle_other1.9616.445720
X-RAY DIFFRACTIONr_scbond_it1.4794.5294670
X-RAY DIFFRACTIONr_scbond_other1.4784.5294670
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8396.716780
X-RAY DIFFRACTIONr_long_range_B_refined2.54733.62210323
X-RAY DIFFRACTIONr_long_range_B_other2.54733.62610324
X-RAY DIFFRACTIONr_rigid_bond_restr0.571318179
X-RAY DIFFRACTIONr_sphericity_free23.4015136
X-RAY DIFFRACTIONr_sphericity_bonded14.323518313
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 370 -
Rwork0.298 7027 -
obs--96.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19360.27140.01920.5439-0.04740.1377-0.02490.05350.02250.01450.02610.04270.0037-0.0491-0.00120.09810.02120.01460.12070.00720.0058195.20166.104534.2866
20.19340.2827-0.03020.5593-0.03050.1208-0.0190.02010.02030.06970.01860.045-0.0626-0.01110.00050.10610.01930.00370.10370.01240.0079212.232995.982836.7553
30.7501-0.04680.03630.0492-0.04050.17910.0389-0.0185-0.05930.0141-0.04370.00270.0402-0.03440.00480.1338-0.0079-0.01030.0737-0.00640.0068242.007985.05261.2117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 384
2X-RAY DIFFRACTION2B4 - 384
3X-RAY DIFFRACTION3C3 - 384

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