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- PDB-8t7l: Copper bound HftA from Treponema denticola -

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Basic information

Entry
Database: PDB / ID: 8t7l
TitleCopper bound HftA from Treponema denticola
ComponentsPathogen-specific surface antigen, putative
KeywordsMETAL BINDING PROTEIN / Lipoprotein / Iron transport / Periplasmic
Function / homologyPeriplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / COPPER (II) ION / Pathogen-specific surface antigen, putative
Function and homology information
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCorbett, B.W. / Suits, M.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-05457 Canada
CitationJournal: To Be Published
Title: Structural and functional characterization of the high-affinity ferrous iron transport protein HftA from Treponema denticola
Authors: Corbett, B.W. / Suits, M.D.
History
DepositionJun 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pathogen-specific surface antigen, putative
B: Pathogen-specific surface antigen, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8805
Polymers34,6562
Non-polymers2233
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-59 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.510, 78.160, 150.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Pathogen-specific surface antigen, putative


Mass: 17328.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: TDE_1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73MJ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: Sodium citrate, Ammonium sulphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.89→42.17 Å / Num. obs: 30767 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 33.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Net I/σ(I): 11.9
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.08 / Num. unique obs: 1100 / CC1/2: 0.997 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PJL

3pjl


Resolution: 1.89→42.17 Å / SU ML: 0.2356 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.4986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1467 4.77 %RANDOM
Rwork0.2079 29295 --
obs0.2091 30762 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.66 Å2
Refinement stepCycle: LAST / Resolution: 1.89→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 7 85 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072508
X-RAY DIFFRACTIONf_angle_d0.91253407
X-RAY DIFFRACTIONf_chiral_restr0.0651343
X-RAY DIFFRACTIONf_plane_restr0.0083453
X-RAY DIFFRACTIONf_dihedral_angle_d7.1231328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.960.30741310.26812914X-RAY DIFFRACTION100
1.96-2.040.23531350.22162831X-RAY DIFFRACTION99.93
2.04-2.130.24531480.20642917X-RAY DIFFRACTION99.97
2.13-2.240.26521580.21292866X-RAY DIFFRACTION100
2.24-2.380.22771420.21372888X-RAY DIFFRACTION100
2.38-2.560.28591450.22192893X-RAY DIFFRACTION99.97
2.57-2.820.25641470.23222938X-RAY DIFFRACTION99.97
2.82-3.230.2521740.22552907X-RAY DIFFRACTION100
3.23-4.070.2171380.19692977X-RAY DIFFRACTION99.97
4.07-42.170.20461490.19163164X-RAY DIFFRACTION99.97

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