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- PDB-6qro: Crystal structure of Tannerella forsythia glutaminyl cyclase -

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Basic information

Entry
Database: PDB / ID: 6qro
TitleCrystal structure of Tannerella forsythia glutaminyl cyclase
ComponentsGlutamine cyclotransferase
KeywordsTRANSFERASE / pyroglutamate formation / Glutaminyl-peptide cyclotransferase / globular alpha/beta-hydrolase fold / Zinc ion
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / acyltransferase activity / hydrolase activity / metal ion binding
Similarity search - Function
Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidase, M28 family
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLinnert, M. / Piechotta, A. / Parthier, C. / Taudte, N. / Kolenko, P. / Rahfeld, J. / Potempa, J. / Stubbs, M.T.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis.
Authors: Taudte, N. / Linnert, M. / Rahfeld, J.U. / Piechotta, A. / Ramsbeck, D. / Buchholz, M. / Kolenko, P. / Parthier, C. / Houston, J.A. / Veillard, F. / Eick, S. / Potempa, J. / Schilling, S. / ...Authors: Taudte, N. / Linnert, M. / Rahfeld, J.U. / Piechotta, A. / Ramsbeck, D. / Buchholz, M. / Kolenko, P. / Parthier, C. / Houston, J.A. / Veillard, F. / Eick, S. / Potempa, J. / Schilling, S. / Demuth, H.U. / Stubbs, M.T.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation_author
Revision 2.0Dec 30, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_site / struct_site_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.pdbx_overall_phase_error / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.pdbx_rms / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _reflns.d_resolution_low / _reflns_shell.d_res_low / _reflns_shell.number_measured_obs / _reflns_shell.number_possible / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _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 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.selection_details
Description: Polymer geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine cyclotransferase
B: Glutamine cyclotransferase
C: Glutamine cyclotransferase
D: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,67521
Polymers142,1654
Non-polymers1,51017
Water10,791599
1
A: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7994
Polymers35,5411
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8955
Polymers35,5411
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8955
Polymers35,5411
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0877
Polymers35,5411
Non-polymers5466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.070, 79.240, 83.080
Angle α, β, γ (deg.)89.940, 90.000, 71.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 44 - 334 / Label seq-ID: 27 - 317

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Glutamine cyclotransferase


Mass: 35541.246 Da / Num. of mol.: 4 / Mutation: H333EK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338) (bacteria)
Strain: ATCC 43037 / JCM 10827 / FDC 338 / Gene: BFO_1693 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLysS
References: UniProt: G8UMP8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: sodium acetate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 2.1→43.92 Å / Num. obs: 76211 / % possible obs: 96 % / Redundancy: 3.592 % / Biso Wilson estimate: 23.251 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.147 / Χ2: 0.916 / Net I/σ(I): 10.15 / Num. measured all: 273764 / Scaling rejects: 131
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.22.6450.462.44208741031778930.6360.58276.5
2.2-2.33.3230.43.4827640864483180.7810.47896.2
2.3-2.53.7050.3254.544896313354132150.8790.37999
2.5-2.73.7290.2375.9935962970896430.9350.27699.3
2.7-33.7670.1747.943786610096100530.9620.20399.6
3-43.7730.08115.775931315791157200.9920.09499.6
4-63.790.05223.7530297804479930.9960.06199.4
6-103.8310.04624.6110213267626660.9980.05499.6
10-43.923.7130.02934.2426367367100.9990.03496.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AFM

2afm


Resolution: 2.1→43.92 Å / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 18.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2011 3939 5.17 %
Rwork0.1736 72400 -
obs0.1795 76211 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.02 Å2 / Biso mean: 16.6025 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 2.1→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 69 599 9908
Biso mean--22.73 15.71 -
Num. residues----1164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5539X-RAY DIFFRACTION14.294TORSIONAL
12B5539X-RAY DIFFRACTION14.294TORSIONAL
13C5539X-RAY DIFFRACTION14.294TORSIONAL
14D5539X-RAY DIFFRACTION14.294TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.140.29071390.22032637277666
2.14-2.180.2671540.2222932308674
2.18-2.220.22311730.2023291346483
2.22-2.260.23221930.20453659385292
2.26-2.310.2351940.18843685387994
2.31-2.370.22451960.19353726392294
2.37-2.420.2421970.1943746394394
2.42-2.490.22921970.18673741393894
2.49-2.560.20781980.18323768396694
2.56-2.650.2141970.18553739393694
2.65-2.740.20651960.18683730392694
2.74-2.850.20221980.17763754395295
2.85-2.980.23061980.17573754395295
2.98-3.140.20691990.17593782398195
3.14-3.330.19571960.17833738393495
3.33-3.590.19371980.17393751394994
3.59-3.950.19881970.16173754395195
3.95-4.520.16581950.1523693388894
4.52-5.70.18071990.16293780397995
5.7-43.920.1791970.17663740393794

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