4EQB | pdb_00004eqb

1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein PotD from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1POT	pdb entry 1POT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	Protein: 0.3M Sodium chloride, 0.01M HEPES; Screen: 0.2M Lithium citrate, 2% Tascimate, 20% (w/v) PEG 3350; Cryo: paratone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.635	α = 75.83
b = 54.347	β = 80.87
c = 76.704	γ = 77.56

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2012-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.5	30	96.8	0.044	33.2	5.9	107591	107591		-3	18.8

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	1.5	1.53	95.6		0.554	3.2	4.9	5284

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	THROUGHOUT	pdb entry 1POT	1.5	29.1	102120	102120	5324	96.75	0.15651	0.15651	0.15498	0.16	0.18554	0.19	RANDOM	17.102

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]
0.19	-0.37	0.19	0.23	0.43	-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.043
r_dihedral_angle_4_deg	15.416
r_dihedral_angle_3_deg	10.585
r_scangle_it	4.656
r_dihedral_angle_1_deg	3.916
r_scbond_it	3.052
r_mcangle_it	1.9
r_angle_refined_deg	1.471
r_mcbond_it	1.152
r_angle_other_deg	0.915

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.043
r_dihedral_angle_4_deg	15.416
r_dihedral_angle_3_deg	10.585
r_scangle_it	4.656
r_dihedral_angle_1_deg	3.916
r_scbond_it	3.052
r_mcangle_it	1.9
r_angle_refined_deg	1.471
r_mcbond_it	1.152
r_angle_other_deg	0.915
r_mcbond_other	0.389
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5272
Nucleic Acid Atoms
Solvent Atoms	969
Heterogen Atoms	47

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
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.