3RG2 | pdb_00003rg2

Structure of a two-domain NRPS fusion protein containing the EntE adenylation domain and EntB aryl-carrier protein from enterobactin biosynthesis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MD9	Mutated DhbE (pdb code 1MD9) with C-terminal domain rotated and pdb entry code 2FQ1
experimental model	PDB	2FQ1	Mutated DhbE (pdb code 1MD9) with C-terminal domain rotated and pdb entry code 2FQ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	6	293	1:1 mixture of protein and 20-30% PEG 3350, 100 mM NH4I, 50 mM MES , pH 6.0, microbatch under oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.575	α = 90
b = 101.771	β = 107.06
c = 240.678	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	MARMOSAIC 325 mm CCD	SSRL 11-1	2007-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.1	40	99.4	0.068	13	3.7	135141	134330		-3	90

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.2	100		0.474	1.8	3.7	12070

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	Mutated DhbE (pdb code 1MD9) with C-terminal domain rotated and pdb entry code 2FQ1	3.1	39.269	1.34	135717	134306	6385	98.96	0.2203	0.2179	0.21	0.2639	0.26	Rfree chosen in thin shells with SHELX

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.4217		-0.6087	3.9582		-5.3798

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.753
f_angle_d	1.356
f_chiral_restr	0.084
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	44567
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	545

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
BALBES	phasing
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.