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- PDB-6qpk: Zt-KP6-1: an effector from Zymoseptoria tritici -

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Basic information

Entry
Database: PDB / ID: 6qpk
TitleZt-KP6-1: an effector from Zymoseptoria tritici
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Effector from Zymoseptoria
Function / homologyCITRIC ACID / Cyanovirin-N domain-containing protein
Function and homology information
Biological speciesZymoseptoria tritici ST99CH_1E4 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsPadilla, A. / Hoh, F. / De guillen, K.
CitationJournal: To Be Published
Title: Structure of ZtMax: an effector from Zymoseptoria
Authors: Padilla, A. / Hoh, F. / De guillen, K.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 4, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / entity / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine / refine_hist / reflns / reflns_shell / software / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_netI_over_av_sigmaI / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _software.classification / _software.name / _software.version / _struct_ref_seq_dif.mon_id / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Polymer backbone linkage / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0189
Polymers18,1622
Non-polymers8557
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-63 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.395, 57.294, 79.355
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 9081.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymoseptoria tritici ST99CH_1E4 (fungus)
Gene: ZT1E4_G3693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H1G421

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 0,1M Tris pH 9, 1.5M LiSO4

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Data collection

DiffractionMean temperature: 270 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.36→46.45 Å / Num. obs: 448165 / % possible obs: 91.3 % / Redundancy: 6.01 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.7
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5272 / CC1/2: 0.45 / % possible all: 56.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimless0.6.3data scaling
HKL2Mapphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.36→46.45 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18 --RANDOM
Rwork0.14 ---
obs0.14 33668 90 %-
Displacement parametersBiso max: 94.57 Å2 / Biso mean: 21.8445 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: LAST / Resolution: 1.36→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 49 265 1565

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