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- PDB-8ehd: Structure of Tannerella forsythia potempin E -

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Basic information

Entry
Database: PDB / ID: 8ehd
TitleStructure of Tannerella forsythia 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0762
Polymers14,8371
Non-polymers2381
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.920, 36.560, 37.160
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

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Components

#1: Protein Potempin E (PotE)


Mass: 14837.278 Da / Num. of mol.: 1
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Native PotE at 9.2 mg/mL in 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 20% (w/v) PEG 8,000, 100 mM Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.8→41.9 Å / Num. obs: 10402 / % possible obs: 98.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1541 / CC1/2: 0.88 / Rrim(I) all: 0.56 / % possible all: 91.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EHC

8ehc


Resolution: 1.8→35.78 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.201 549 5.28 %RANDOM
Rwork0.184 ---
obs0.185 10401 98.3 %-
Displacement parametersBiso mean: 30.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.1162 Å20 Å2-0.7545 Å2
2---11.6195 Å20 Å2
3---7.5032 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.8→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 15 88 953
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01899HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.951219HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d418SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes126HARMONIC5
X-RAY DIFFRACTIONt_it899HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion2.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion111SEMIHARMONIC5
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_contact1074SEMIHARMONIC4
LS refinement shellResolution: 1.8→2.01 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2447 155 5.49 %
Rwork0.2168 2668 -
all0.2182 2823 -
obs--95.08 %
Refinement TLS params.Method: refined / Origin x: -15.0505 Å / Origin y: -18.5007 Å / Origin z: 13.0753 Å
111213212223313233
T-0.0204 Å2-0.0002 Å20.0003 Å2--0.0004 Å2-0.002 Å2--0.0332 Å2
L1.0309 °2-0.2453 °20.3077 °2-0.6894 °20.0424 °2--2.4037 °2
S-0.0336 Å °0.0314 Å °0.0087 Å °-0.0623 Å °-0.0328 Å °0.0029 Å °-0.0709 Å °-0.1641 Å °0.0664 Å °
Refinement TLS groupSelection details: {A|27 - 127}

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