9CLY | pdb_00009cly

Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R

PDB DOI: https://doi.org/10.2210/pdb9CLY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus agalactiae 2603V/R
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-12 Released: 2024-07-24
Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R

Maltseva, N., Kim, Y., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 54.83 kDa
Atom Count: 4,053
Modeled Residue Count: 482
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CylG protein	A, B	243	Streptococcus agalactiae 2603V/R	Mutation(s): 0 Gene Names: cylG, SAG0664
UniProt
Find proteins for Q8E0R2 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8E0R2 Go to UniProtKB: Q8E0R2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E0R2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.202 (Depositor), 0.203 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.518	α = 90
b = 111.518	β = 90
c = 102.561	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.