2PS3 | pdb_00002ps3

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PS0	PDB entry 2PS0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	5 mg/mL protein in 20 mM MOPS, pH 7.0, 5 mM EDTA, 20 mM NaCl, 5 % glycerol was mixed 1:1 with a cryoprotectant solution containing 35.5 % (w/v) PEG 4000, 0.2 M ammonium acetate, 9 % glycerol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.875	α = 90
b = 89.842	β = 90
c = 91.556	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	2006-07-06	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	2.45	35.1	98.7	0.084		6.6		20560			58.3

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)
	2.45	2.54	90.4		0.3		4.4	1855

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 (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 2PS0	2.47	35.1	20560	20515	1068	97.97	0.243	0.24	0.24	0.303	0.3	RANDOM	58.271

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]
3.69			-5.13		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.999
r_dihedral_angle_4_deg	21.929
r_dihedral_angle_3_deg	16.684
r_dihedral_angle_1_deg	5.479
r_scangle_it	2.152
r_scbond_it	1.366
r_angle_refined_deg	1.341
r_mcangle_it	1.19
r_mcbond_it	0.672
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.999
r_dihedral_angle_4_deg	21.929
r_dihedral_angle_3_deg	16.684
r_dihedral_angle_1_deg	5.479
r_scangle_it	2.152
r_scbond_it	1.366
r_angle_refined_deg	1.341
r_mcangle_it	1.19
r_mcbond_it	0.672
r_nbtor_refined	0.308
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.228
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4066
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

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

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.