1VLG

Crystal structure of Ferritin (TM1128) from Thermotoga maritima at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VLG/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-07-23 Released: 2004-08-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.218 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of Ferritin (TM1128) from Thermotoga maritima at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 169.53 kDa
Atom Count: 11,751
Modelled Residue Count: 1,312
Deposited Residue Count: 1,408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ferritin	A, B, C, D, E A, B, C, D, E, F, G, H	176	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM1128 EC: 1.16.3.2
UniProt
Find proteins for Q9X0L2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0L2 Go to UniProtKB: Q9X0L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X0L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain X [auth D] SDF format, chain J [auth A] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	AA [auth E] BA [auth E] FA [auth F] J [auth A] K [auth A] AA [auth E], BA [auth E], FA [auth F], J [auth A], K [auth A], L [auth A], LA [auth H], M [auth A], O [auth B], P [auth B], Q [auth B], U [auth C], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain MA [auth H] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C]	CA [auth E] DA [auth E] GA [auth F] HA [auth F] JA [auth G] CA [auth E], DA [auth E], GA [auth F], HA [auth F], JA [auth G], MA [auth H], R [auth B], S [auth B], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	EA [auth F] I [auth A] IA [auth G] KA [auth H] N [auth B] EA [auth F], I [auth A], IA [auth G], KA [auth H], N [auth B], T [auth C], W [auth D], Z [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31VLG

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.634	α = 90
b = 175.634	β = 90
c = 354.843	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOLREP	phasing
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-08-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-08-17
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Data collection
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2023-09-20
Changes: Data collection, Refinement description