6NCI | pdb_00006nci

Crystal structure of CDP-Chase: Vector data collection

• PDB DOI: https://doi.org/10.2210/pdb6NCI/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-11 Released: 2019-02-06 
• Deposition Author(s): Miller, M.S., Shi, W., Gabelli, S.B.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.223 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.

Miller, M.S., Maheshwari, S., Shi, W., Gao, Y., Chu, N., Soares, A.S., Cole, P.A., Amzel, L.M., Fuchs, M.R., Jakoncic, J., Gabelli, S.B.

(2019) Molecules 24

• PubMed: 30704096 
• DOI: https://doi.org/10.3390/molecules24030496
• Primary Citation Related Structures: 
  6NCH, 6NCI, 6NCK, 6NCT


• PubMed Abstract: 
  

  Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins-Akt1, PI3Kα, and CDP-Chase-to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or "raster-collect", a more automated approach for a larger number of crystals (using CDP-Chase as an example).

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Organizational Affiliation: 
• Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].
Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. [e-mail].
Case Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA. [e-mail].
Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. [e-mail].
Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. [e-mail].
Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. [e-mail].
Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].
Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. [e-mail].
Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. [e-mail].
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].
Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.37 kDa 
• Atom Count: 3,595 
• Modeled Residue Count: 401 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphohydrolase (MutT/nudix family protein)	A, B	205	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_2032
UniProt
Find proteins for Q81EE8 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81EE8  Go to UniProtKB:  Q81EE8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB5 (Subject of Investigation/LOI)	I [auth B]	D-ribose C5 H10 O5 PYMYPHUHKUWMLA-LMVFSUKVSA-N
PEG	H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4 (Subject of Investigation/LOI)	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.223 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.771	α = 90
b = 67.008	β = 90
c = 111.426	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Miller, M.S., Shi, W., Gabelli, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA062924

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-01
  Changes: Atomic model
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description