3DDJ | pdb_00003ddj

Crystal structure of a cbs domain-containing protein in complex with amp (sso3205) from sulfolobus solfataricus at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DDJ/pdb

• Classification: AMP-BINDING PROTEIN
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-05 Released: 2008-06-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of CBS domain-containing protein in complex with AMP (NP_344512.1) from SULFOLOBUS SOLFATARICUS at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

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: 34.53 kDa 
• Atom Count: 2,551 
• Modeled Residue Count: 279 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein	A	296	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: NP_344512.1, SSO3205
UniProt
Find proteins for Q97U20 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97U20  Go to UniProtKB:  Q97U20

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DDJ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.56	α = 90
b = 48.09	β = 93.83
c = 83.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary