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- PDB-2fjc: Crystal structure of antigen TpF1 from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 2fjc
TitleCrystal structure of antigen TpF1 from Treponema pallidum
ComponentsAntigen TpF1
KeywordsMETAL TRANSPORT / Mini ferritin / iron binding protein / antigen
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThumiger, A. / Polenghi, A. / Papinutto, E. / Battistutta, R. / Montecucco, C. / Zanotti, G.
Citation
Journal: Proteins / Year: 2006
Title: Crystal structure of antigen TpF1 from Treponema pallidum.
Authors: Thumiger, A. / Polenghi, A. / Papinutto, E. / Battistutta, R. / Montecucco, C. / Zanotti, G.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structure of the neutrophil-activating protein from Helicobacter pylori
Authors: Zanotti, G. / Papinutto, E. / Dundon, W. / Battistutta, R. / Seveso, M. / Giudice, G. / Rappuoli, R. / Montecucco, C.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 1998
Title: The crystal structure of Dps, a ferritin homologue that binds and protects DNA
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
#3: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: The dodecameric ferritin from listeria innocua contains a novel intersubunit iron-binding site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
#4: Journal: J.Biol.Chem. / Year: 2002
Title: Structure of two iron-binding proteins from Bacillus anthracis
Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen TpF1
B: Antigen TpF1
C: Antigen TpF1
D: Antigen TpF1
E: Antigen TpF1
F: Antigen TpF1
G: Antigen TpF1
H: Antigen TpF1
I: Antigen TpF1
J: Antigen TpF1
K: Antigen TpF1
L: Antigen TpF1
M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,93632
Polymers276,04216
Non-polymers89416
Water9,314517
1
A: Antigen TpF1
B: Antigen TpF1
C: Antigen TpF1
D: Antigen TpF1
E: Antigen TpF1
F: Antigen TpF1
G: Antigen TpF1
H: Antigen TpF1
I: Antigen TpF1
J: Antigen TpF1
K: Antigen TpF1
L: Antigen TpF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,70224
Polymers207,03212
Non-polymers67012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38430 Å2
ΔGint-405 kcal/mol
Surface area61210 Å2
MethodPISA
2
M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules

M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules

M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,70224
Polymers207,03212
Non-polymers67012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
3
M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules

M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules

M: Antigen TpF1
N: Antigen TpF1
O: Antigen TpF1
P: Antigen TpF1
hetero molecules

A: Antigen TpF1
B: Antigen TpF1
C: Antigen TpF1
D: Antigen TpF1
E: Antigen TpF1
F: Antigen TpF1
G: Antigen TpF1
H: Antigen TpF1
I: Antigen TpF1
J: Antigen TpF1
K: Antigen TpF1
L: Antigen TpF1
hetero molecules

A: Antigen TpF1
B: Antigen TpF1
C: Antigen TpF1
D: Antigen TpF1
E: Antigen TpF1
F: Antigen TpF1
G: Antigen TpF1
H: Antigen TpF1
I: Antigen TpF1
J: Antigen TpF1
K: Antigen TpF1
L: Antigen TpF1
hetero molecules

A: Antigen TpF1
B: Antigen TpF1
C: Antigen TpF1
D: Antigen TpF1
E: Antigen TpF1
F: Antigen TpF1
G: Antigen TpF1
H: Antigen TpF1
I: Antigen TpF1
J: Antigen TpF1
K: Antigen TpF1
L: Antigen TpF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)830,80896
Polymers828,12748
Non-polymers2,68148
Water86548
TypeNameSymmetry operationNumber
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_666x-y+1,-y+1,-z+11
crystal symmetry operation6_656-x+1,-x+y,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area160560 Å2
ΔGint-1667 kcal/mol
Surface area238150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.921, 184.921, 154.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
Antigen TpF1 / Antigen C1-5 / Antigen 4D


Mass: 17252.652 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tpf1 / Plasmid: pSM214G-TpF1 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl 1blue / References: UniProt: P16665
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 6000, 8% ethylene glycol, 0.1 M Tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.45→185 Å / Num. all: 111030 / Num. obs: 111030 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.5
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.5 / Num. unique all: 11886 / % possible all: 70.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JI4

1ji4


Resolution: 2.5→59.37 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1010942.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 10614 10.1 %RANDOM
Rwork0.227 ---
obs0.227 105521 99.9 %-
all-105521 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4013 Å2 / ksol: 0.349013 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å24.95 Å20 Å2
2--0.4 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18986 0 16 517 19519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.862.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 1788 10.3 %
Rwork0.303 15632 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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