3CTD

Crystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris

• PDB DOI: https://doi.org/10.2210/pdb3CTD/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Prochlorococcus marinus subsp. pastoris str. CCMP1986
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-04-11 Released: 2008-04-29 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., 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: 2.50 Å
• R-Value Free: 
  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris.

Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 48.32 kDa 
• Atom Count: 2,435 
• Modelled Residue Count: 308 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ATPase, AAA family	A, B	213	Prochlorococcus marinus subsp. pastoris str. CCMP1986	Mutation(s): 1  Gene Names: yrvN, PMM0077
UniProt
Find proteins for Q7V3J8 (Prochlorococcus marinus subsp. pastoris (strain CCMP1986 / NIES-2087 / MED4)) Explore Q7V3J8  Go to UniProtKB:  Q7V3J8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.184	α = 90
b = 108.184	β = 90
c = 68.685	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: 2008-04-29 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., 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: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection