2PS0 | pdb_00002ps0

Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.9	293	30 % (w/v) PEG 4000, 5 % isopropanol, 0.1 M succinate, pH 4.9 mixed 1:1 with 10 mg/mL ZnZnuA or 1:2 with 2.5 mg/mL ZnZnuA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.438	α = 90
b = 86.266	β = 90
c = 88.147	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate	mirrors	2006-03-03	M	SINGLE WAVELENGTH
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B		APS	5ID-B
2	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID
3	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2	37.2	99.8	0.082		6.8		38461			28.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	98.4		0.289		5.8	3729

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2	37.2	38461	38401	1925	99.75	0.201	0.199	0.1994	0.25	0.2483	RANDOM	28.835

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]
2.13			0.32		-2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.114
r_dihedral_angle_4_deg	15.846
r_dihedral_angle_3_deg	15.193
r_dihedral_angle_1_deg	5.683
r_scangle_it	2.639
r_scbond_it	1.582
r_angle_refined_deg	1.188
r_mcangle_it	1.188
r_mcbond_it	0.681
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.114
r_dihedral_angle_4_deg	15.846
r_dihedral_angle_3_deg	15.193
r_dihedral_angle_1_deg	5.683
r_scangle_it	2.639
r_scbond_it	1.582
r_angle_refined_deg	1.188
r_mcangle_it	1.188
r_mcbond_it	0.681
r_nbtor_refined	0.297
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.085
r_metal_ion_refined	0.049
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4090
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
SHELXS	phasing

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.