2XIG | pdb_00002xig

The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		ZN-SAD MODEL AT 2.15A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		HPFUR2M PRE-LOADED WITH ZINC (2 EQ) AT 30 MG/ML WAS CRYSTALLIZED FROM 20% PEG 3350, 100 MM NA CITRATE, pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.34	45.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.15	α = 83.32
b = 48.29	β = 77.82
c = 72.25	γ = 87.65

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	ADSC QUANTUM 315	TOROIDAL MIRROR	2009-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.85	47.96	95.2	0.1	4.5	4.1		51362		6	23.58

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	1.85	1.95	94.8		0.39	1.8	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	ZN-SAD MODEL AT 2.15A	1.85	35.097	1.96	99642	5032	92.4	0.1999	0.1981	0.19	0.2339	0.23	35.66

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]
5.3609	3.9897	-2.2187	4.5069	-2.4059	-9.8678

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.233
f_angle_d	0.87
f_chiral_restr	0.061
f_bond_d	0.005
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4780
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	25

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	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.