3GG7 | pdb_00003gg7

Crystal structure of an uncharacterized metalloprotein from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb3GG7/pdb

• Classification: structural genomics, unknown function
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-27 Released: 2009-03-24 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of an uncharacterized metalloprotein from Deinococcus radiodurans

Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 28.97 kDa 
• Atom Count: 2,086 
• Modeled Residue Count: 243 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized metalloprotein	A	254	Deinococcus radiodurans	Mutation(s): 0  Gene Names: DR_C0006
UniProt
Find proteins for Q9RZH8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RZH8  Go to UniProtKB:  Q9RZH8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	F [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.207	α = 90
b = 47.207	β = 90
c = 97.787	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references