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- PDB-8ehc: Structure of Tannerella forsythia selenomethionine-derivatized po... -

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Basic information

Entry
Database: PDB / ID: 8ehc
TitleStructure of Tannerella forsythia selenomethionine-derivatized potempin E
ComponentsPotempin E (PotE)
KeywordsHYDROLASE INHIBITOR / Metallopeptidase inhibitor / HYDROLASE
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2023
Title: A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia.
Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. ...Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. / Enghild, J.J. / Cuppari, A. / Arolas, J.L. / de Diego, I. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T. / Dive, V. / Zani, M.L. / Moreau, T. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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 / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potempin E (PotE)
B: Potempin E (PotE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6234
Polymers23,4382
Non-polymers1842
Water1,928107
1
A: Potempin E (PotE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8112
Polymers11,7191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Potempin E (PotE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8112
Polymers11,7191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.130, 71.350, 39.150
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Potempin E (PotE)


Mass: 11719.185 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: TFUB20_00705 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UL35
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Selenomethionine-derivatised PotE at 10 mg/mL in 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 20% (w/v) PEG 1,000, 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2→71.3 Å / Num. obs: 25564 / % possible obs: 94.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.083 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2008 / CC1/2: 0.72 / Rrim(I) all: 0.589 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.178
RfactorNum. reflection% reflectionSelection details
Rfree0.251 658 4.79 %RANDOM
Rwork0.193 ---
obs0.196 13728 99.1 %-
Displacement parametersBiso mean: 33.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.8094 Å20 Å2-0.5181 Å2
2---2.1767 Å20 Å2
3----0.6327 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 12 107 1724
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072236HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d758SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes228HARMONIC5
X-RAY DIFFRACTIONt_it1657HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion2.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion207SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1894SEMIHARMONIC4
LS refinement shellResolution: 2→2.16 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3131 104 3.67 %
Rwork0.222 2733 -
all0.2252 2837 -
obs--99.27 %
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)
13.78290.1477-0.89941.08410.62551.8268-0.059-0.1425-0.24680.0528-0.00440.00390.1238-0.00410.0633-0.02290.0148-0.0514-0.02560.03530.058511.174327.024445.3082
22.76530.37760.21721.3834-0.39521.10260.1177-0.10690.15180.0697-0.05190.0461-0.0694-0.0346-0.0658-0.02490.0028-0.0347-0.038-0.02080.05129.425140.163625.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|31 - 127}
2X-RAY DIFFRACTION2{B|31 - 127}

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