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

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Basic information

Entry
Database: PDB / ID: 8ehb
TitleStructure of Tannerella forsythia selenomethionine-derivatized potempin D mutant I53M
ComponentsPutative lipoprotein
KeywordsHYDROLASE INHIBITOR / Metallopeptidase inhibitor / HYDROLASE
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Putative lipoprotein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Other government
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 1.2Mar 20, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3Nov 6, 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: Putative lipoprotein
B: Putative lipoprotein
C: Putative lipoprotein
D: Putative lipoprotein
E: Putative lipoprotein
F: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9517
Polymers78,8896
Non-polymers621
Water1,18966
1
A: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)13,1481
Polymers13,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)13,1481
Polymers13,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)13,1481
Polymers13,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2102
Polymers13,1481
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)13,1481
Polymers13,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)13,1481
Polymers13,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.960, 78.150, 71.460
Angle α, β, γ (deg.)90.000, 117.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 29 through 125)
d_2ens_1(chain "B" and resid 29 through 125)
d_3ens_1(chain "C" and resid 29 through 125)
d_4ens_1(chain "D" and resid 29 through 125)
d_5ens_1chain "E"
d_6ens_1(chain "F" and resid 29 through 125)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSLYSA6 - 102
d_21ens_1CYSLYSB4 - 100
d_31ens_1CYSLYSC6 - 102
d_41ens_1CYSLYSD4 - 100
d_51ens_1CYSLYSE1 - 97
d_61ens_1CYSLYSF2 - 98

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Components

#1: Protein
Putative lipoprotein


Mass: 13148.148 Da / Num. of mol.: 6 / Mutation: I53M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338) (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338
Gene: BFO_2662 / Production host: Escherichia coli (E. coli) / References: UniProt: G8ULV2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Isolated selenomethionine-derivatised PotD mutant I53M at 14 mgL in 5 mM Tris-HCl, 50 mM sodium chloride, 0.02% sodium azide pH 8.0 was crystallised with 20% PEG 3350, 0.2 M diammonium ...Details: Isolated selenomethionine-derivatised PotD mutant I53M at 14 mgL in 5 mM Tris-HCl, 50 mM sodium chloride, 0.02% sodium azide pH 8.0 was crystallised with 20% PEG 3350, 0.2 M diammonium hydrogen citrate as reservoir solution

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→63.2 Å / Num. obs: 27047 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.55 Å / Rmerge(I) obs: 1.517 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 4462 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.4→63.2 Å / SU ML: 0.3908 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.0272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 531 1.97 %
Rwork0.2177 26453 -
obs0.218 26984 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→63.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 4 66 5014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945053
X-RAY DIFFRACTIONf_angle_d1.20126788
X-RAY DIFFRACTIONf_chiral_restr0.0681731
X-RAY DIFFRACTIONf_plane_restr0.0095857
X-RAY DIFFRACTIONf_dihedral_angle_d12.42072007
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.76100053282
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.632918698662
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS2.13386665557
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.4023591259
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.62050876219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.35611490.31686559X-RAY DIFFRACTION98.91
2.64-3.020.29271230.28416575X-RAY DIFFRACTION99.33
3.02-3.810.24521270.22486613X-RAY DIFFRACTION99.5
3.81-63.20.19321320.17916706X-RAY DIFFRACTION99.4
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)
14.66594742131-0.618435323505-1.782366042172.163135853481.661553533124.07253634905-0.1629005854130.0482886841405-0.2474943447680.1994125339250.1480404672820.1550660567360.283883196205-0.3828279589060.0009886129670880.43927212617-0.00278189583538-0.02181264089180.4782499578290.08546651706570.4081792887372.909020162361.638520227047.91714298
22.475330579462.70866878283-1.027556590155.37760996223-0.6586786584622.03429600772-0.04552889039030.2687800091390.09280797688960.05456454366540.005987381163060.14141131255-6.69273855523E-5-0.0850430692232-0.00279877021220.453368921591-0.00530840062591-0.05893752020150.4836342229890.01077082446730.521055629752-1.68611203731-11.4000475307-9.76230294702
35.046731484550.531422475419-1.387146882712.30909749323-1.757694286395.17013699369-0.203036044459-0.0432414689147-0.251911954228-0.2065087296310.236451670838-0.1954575003670.4997164450830.260922614413-0.0002711935622010.468194500660.0125206540289-0.01576801932360.349462782133-0.06312164793490.40647496548232.27254875120.755377697595-7.68868079503
43.75513029944-2.71731750622-1.087029444835.606854038470.7718164005061.2257333432-0.116486347007-0.3156331603240.1068191955560.008470157915910.0579676234897-0.0802011688314-0.00204607218283-0.15102978086-0.004123894416130.4318751849670.0446035020876-0.04317897432290.433612941628-0.02498273704080.44681623996536.7853404432-12.36276548839.8414237819
56.5586398314-0.326459298898-1.786299570012.442510524331.226056293115.643754871080.3500773941410.4083800751170.367193216201-0.0542224464549-0.1063737112660.120866526911-0.146764180156-0.1361892780588.59626225758E-50.4945088072360.009591142334110.006393123479130.5391283884210.02736970677370.47998022567213.43165597147.87229327935-31.0581248463
64.917940932550.594263657621-0.7925661065481.799825438490.2995813590414.366325527490.194514269904-0.7486435156130.132702917377-0.02225923240520.10428650275-0.1242148145440.04822279569280.101338846863-0.001295824020260.5185283857730.098880544207-0.02707490097960.65268669936-0.05186080419550.512173226832-15.39316314066.07701544696-31.5476720831
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 24 through 125)AA24 - 1251 - 102
22(chain 'B' and resid 26 through 125)BB26 - 1251 - 100
33(chain 'C' and resid 24 through 125)CC24 - 1251 - 102
44(chain 'D' and resid 26 through 125)DD26 - 1251 - 100
55(chain 'E' and resid 29 through 125)EE29 - 1251 - 97
66(chain 'F' and resid 28 through 125)FF28 - 1251 - 98

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