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- PDB-6qql: Crystal structure of Porphyromonas gingivalis glutaminyl cyclase -

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Basic information

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


acyltransferase activity
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
Glutamine cyclotransferase-related protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.814 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 18, 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 1.2Dec 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 1.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7124
Polymers69,5812
Non-polymers1312
Water1,40578
1
A: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8562
Polymers34,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8562
Polymers34,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.904, 89.904, 164.696
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 41 through 328)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 41 - 328 / Label seq-ID: 25 - 312

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 41 through 328)AA
2chain BBB

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Components

#1: Protein Glutamine cyclotransferase


Mass: 34790.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Gene: PG_2157 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLysS / References: UniProt: Q7MT37
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: HEPES pH 8.0, PEG 400, 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: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.81→44.952 Å / Num. obs: 35878 / % possible obs: 99.3 % / Redundancy: 3.935 % / Biso Wilson estimate: 27.674 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.335 / Rrim(I) all: 0.391 / Χ2: 1.025 / Net I/σ(I): 4.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.81-2.983.91.0681.2557940.4441.24298.7
2.98-3.194.0050.7561.7554560.6430.876100
3.19-3.444.020.5132.5751060.8110.594100
3.44-3.773.6080.3524.3345560.9080.41897.6
3.77-4.213.90.3075.0841860.9190.35898.8
4.21-4.864.0030.1887.4937470.9590.21899.8
4.86-5.934.0670.1866.7931740.9630.215100
5.93-8.314.0650.1767.1624590.970.203100
8.31-44.9523.9460.07614.414000.9940.08899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.66 Å44.95 Å
Translation5.66 Å44.95 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SI0

3si0


Resolution: 2.814→44.952 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.12 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2757 1786 4.98 %
Rwork0.2167 --
obs0.2197 35868 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.99 Å2 / Biso mean: 34.7614 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 2.814→44.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 2 78 4555
Biso mean--79.75 18.71 -
Num. residues----577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2589X-RAY DIFFRACTION10.972TORSIONAL
12B2589X-RAY DIFFRACTION10.972TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8143-2.89040.32631350.27592608274397
2.8904-2.97540.33981400.262126062746100
2.9754-3.07140.36181380.261526012739100
3.0714-3.18120.32071390.241326762815100
3.1812-3.30850.32231360.221626442780100
3.3085-3.4590.2421410.220626542795100
3.459-3.64130.32911380.25812568270699
3.6413-3.86930.33521350.29242578271397
3.8693-4.16790.31661350.21882587272298
4.1679-4.58690.21841400.176126322772100
4.5869-5.24980.20731370.155526392776100
5.2498-6.61080.19481370.170226402777100
6.6108-44.95770.21411350.160626492784100
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)
11.57960.6537-0.09621.3385-0.21451.6114-0.0812-0.0244-0.1866-0.37120.04180.0027-0.06920.00880.03030.1541-0.00490.00270.17760.01140.141941.1292-24.4199181.0871
21.39680.1145-0.01540.920.2231.69540.1729-0.12720.180.1278-0.24510.0601-0.468-0.3813-0.04080.3675-0.06760.11840.25370.04810.017638.3685-11.398188.055
32.10891.88050.01153.2345-0.03091.56120.3294-0.142-0.59360.3652-0.2608-0.5893-0.01150.65060.16540.2337-0.0102-0.01670.40020.13050.314251.8384-31.2608186.9163
40.1646-0.28630.06350.5386-0.18870.4937-0.141-0.2336-0.14440.12640.0661-0.2490.1378-0.00770.02070.2177-0.09990.02530.2727-0.02510.176344.4672-22.9816197.215
50.9789-0.18790.13620.6926-0.15960.76590.1619-0.227-0.09680.1368-0.09050.0196-0.00950.0441-0.03660.1722-0.0151-0.03490.25210.03620.206540.1486-26.1381200.7249
61.4853-0.40940.00871.01690.00381.5136-0.0375-0.028-0.04430.05690.19870.12260.0473-0.2041-0.0840.0812-0.1052-0.01280.32410.08190.188131.9902-23.7755192.305
71.43510.6279-0.10441.36310.07182.034-0.0415-0.1819-0.1009-0.2239-0.18-0.35060.44920.50430.08040.21830.08170.03030.23130.06710.310961.5573-8.9863170.2289
80.84940.0689-0.01671.4642-0.01371.3963-0.1403-0.51420.3732-0.0921-0.323-0.2905-0.04220.2652-0.16670.0633-0.01570.01860.46430.04680.274466.2779-0.7657172.98
90.866-0.2034-0.14681.5293-0.31791.5387-0.0539-0.060.1163-0.3618-0.0405-0.22170.27920.36330.06770.14690.02580.0360.14790.03140.219860.4778-0.9477162.9306
100.12710.24220.04820.6303-0.34550.9809-0.04520.03880.1041-0.0351-0.0085-0.012-0.35920.07180.08630.2557-0.0331-0.07490.18520.0190.248158.294113.4188167.2688
111.6538-0.522-0.07821.15320.0660.446-0.1766-0.28240.4295-0.09280.0026-0.4566-0.54640.1834-0.12340.2818-0.083-0.0280.2240.03890.347964.249712.7762171.7372
121.50090.14520.22071.1084-0.50181.91330.21310.19850.015-0.1006-0.07860.0644-0.03130.25720.0820.1083-0.13820.16270.1626-0.01310.171955.49515.0261176.2825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 150 )A41 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 179 )A151 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 202 )A180 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 237 )A203 - 237
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 294 )A238 - 294
6X-RAY DIFFRACTION6chain 'A' and (resid 295 through 329 )A295 - 329
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 111 )B41 - 111
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 150 )B112 - 150
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 218 )B151 - 218
10X-RAY DIFFRACTION10chain 'B' and (resid 219 through 276 )B219 - 276
11X-RAY DIFFRACTION11chain 'B' and (resid 277 through 294 )B277 - 294
12X-RAY DIFFRACTION12chain 'B' and (resid 295 through 328 )B295 - 328

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