1VJ2 | pdb_00001vj2

Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VJ2/pdb
• Entry: 1VJ2 supersedes: 1O5N

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


• Deposited: 2003-12-03 Released: 2003-12-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.249 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution.

Jaroszewski, L., Schwarzenbacher, R., von Delft, F., McMullan, D., Brinen, L.S., Canaves, J.M., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Eshagi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Hampton, E., Levin, I., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Reyes, R., Rezezadeh, F., Robb, A., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 56: 611-614

• PubMed: 15229893 
• DOI: https://doi.org/10.1002/prot.20130
• Primary Citation Related Structures: 
  1VJ2

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, Stanford University, 2575 Sand Hill Rd, Menlo Park, California, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.29 kDa 
• Atom Count: 2,025 
• Modeled Residue Count: 228 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
novel manganese-containing cupin TM1459	A, B	126	Thermotoga maritima	Mutation(s): 0  Gene Names: TM1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0  Go to UniProtKB:  Q9X1H0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
UNL	D [auth A]	Unknown ligand WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.249 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VJ2

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 52.55	β = 90
c = 96.267	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1O5N

Revision History  

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2023-09-20
  Changes: Data collection, Refinement description