3Q4R | pdb_00003q4r

Crystal Structure of a deletion mutant(11-185) of hypothetical protein MJ0754 with Zn2+

• PDB DOI: https://doi.org/10.2210/pdb3Q4R/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-24 Released: 2011-05-18 
• Deposition Author(s): Hwang, K.Y., Lee, E.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii.

Lee, E.H., Kim, H.S., Kim, H.Y., Jeon, Y.H., Hwang, K.Y.

(2011) Proteins 79: 2358-2363

• PubMed: 21604308 
• DOI: https://doi.org/10.1002/prot.23066
• Primary Citation Related Structures: 
  3Q4N, 3Q4O, 3Q4Q, 3Q4R

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Organizational Affiliation: 
• Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.35 kDa 
• Atom Count: 1,597 
• Modeled Residue Count: 170 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ0754	A	196	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ0754
UniProt
Find proteins for Q58164 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58164  Go to UniProtKB:  Q58164

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	D [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.943	α = 90
b = 80.129	β = 90
c = 93.659	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Hwang, K.Y., Lee, E.H.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-01-01
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description