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- PDB-8t7k: Apo HftA from Treponema denticola -

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Basic information

Entry
Database: PDB / ID: 8t7k
TitleApo 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 / Pathogen-specific surface antigen, putative
Function and homology information
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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


Theoretical massNumber of molelcules
Total (without water)17,2711
Polymers17,2711
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, PISA was used to support the assembly state being monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.735, 74.968, 79.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pathogen-specific surface antigen, putative


Mass: 17271.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: TDE_1511 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73MJ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, ammonium sulphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.78→29.62 Å / Num. obs: 16097 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.2
Reflection shellResolution: 1.78→1.88 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2296 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PJL

3pjl


Resolution: 1.78→29.62 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 747 4.65 %RANDOM
Rwork0.2153 ---
obs0.2163 16053 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 0 53 1273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.909
X-RAY DIFFRACTIONf_dihedral_angle_d7.065164
X-RAY DIFFRACTIONf_chiral_restr0.066172
X-RAY DIFFRACTIONf_plane_restr0.009227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.920.29931350.26123013X-RAY DIFFRACTION100
1.92-2.110.251570.22133040X-RAY DIFFRACTION100
2.11-2.420.24711520.22393013X-RAY DIFFRACTION100
2.42-3.040.2871490.2543055X-RAY DIFFRACTION100
3.04-29.620.21261540.19273185X-RAY DIFFRACTION100

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