3CTP | pdb_00003ctp

Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with D-xylulofuranose

• PDB DOI: https://doi.org/10.2210/pdb3CTP/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Alkaliphilus metalliredigens QYMF
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-14 Released: 2008-05-06 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Wasserman, S.R., Meyer, A., 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: 1.41 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with L-xylulose.

Malashkevich, V.N., Toro, R., Wasserman, S.R., Meyer, A., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

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: 75.1 kDa 
• Atom Count: 4,840 
• Modelled Residue Count: 532 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A, B	330	Alkaliphilus metalliredigens QYMF	Mutation(s): 0  Gene Names: Amet_0586
UniProt
Find proteins for A6TKU5 (Alkaliphilus metalliredigens (strain QYMF)) Explore A6TKU5  Go to UniProtKB:  A6TKU5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XLF	C [auth A], E [auth B]	beta-D-xylulofuranose C5 H10 O5 LQXVFWRQNMEDEE-MROZADKFSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.172	α = 90
b = 61.903	β = 104.81
c = 74.362	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Malashkevich, V.N., Toro, R., Wasserman, S.R., Meyer, A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2021-02-03
  Changes: Database references, Structure summary
• Version 2.2: 2024-02-21
  Changes: Data collection, Database references