2FJC | pdb_00002fjc

Crystal structure of antigen TpF1 from Treponema pallidum

PDB DOI: https://doi.org/10.2210/pdb2FJC/pdb

Classification: METAL TRANSPORT
Organism(s): Treponema pallidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-01-02 Released: 2006-01-10
Deposition Author(s): Thumiger, A., Polenghi, A., Papinutto, E., Battistutta, R., Montecucco, C., Zanotti, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.252 (Depositor), 0.252 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of antigen TpF1 from Treponema pallidum.

Thumiger, A., Polenghi, A., Papinutto, E., Battistutta, R., Montecucco, C., Zanotti, G.

(2006) Proteins 62: 827-830

PubMed: 16345079 Search on PubMed
DOI: https://doi.org/10.1002/prot.20828
Primary Citation Related Structures:
2FJC

Organizational Affiliation

Dipartimento di Scienze Chimiche e ICB-CNR, Università di Padova, Padova, Italy.

Macromolecule Content

Total Structure Weight: 276.94 kDa
Atom Count: 19,519
Modeled Residue Count: 2,416
Deposited Residue Count: 2,496
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen TpF1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	156	Treponema pallidum	Mutation(s): 0 Gene Names: tpf1
UniProt
Find proteins for P16665 (Treponema pallidum (strain Nichols)) Explore P16665 Go to UniProtKB: P16665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain FA [auth P] SDF format, chain EA [auth O] SDF format, chain DA [auth N] SDF format, chain CA [auth M] SDF format, chain BA [auth L] SDF format, chain AA [auth K] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth P] MOL2 format, chain EA [auth O] MOL2 format, chain DA [auth N] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth P] mmCIF format, chain EA [auth O] mmCIF format, chain DA [auth N] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] CA [auth M] DA [auth N] EA [auth O] AA [auth K], BA [auth L], CA [auth M], DA [auth N], EA [auth O], FA [auth P], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.252 (Depositor), 0.252 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.921	α = 90
b = 184.921	β = 90
c = 154.883	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-01-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description