3D41 | pdb_00003d41

Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgAMPPNP and fosfomycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D40	PDB ENTRY 3D40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.656	α = 90
b = 85.656	β = 90
c = 78.979	γ = 120

Symmetry
Space Group	P 32 2 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	MAR CCD 165 mm	mirrors	2007-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CAMD BEAMLINE GCPCC	1.38074	CAMD	GCPCC

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	2.2	50	99.6	0.071	19.2	4.1	17293	17293		-3	46.3

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)
1	2.2	2.28	97.9		0.557	1.8	3.4	1664

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 3D40	2.2	29.04	15587	15587	215	90.97	0.193	0.193	0.19	0.252	0.25	RANDOM	43.194

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]
2.11	1.06		2.11		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.522
r_dihedral_angle_4_deg	21.808
r_dihedral_angle_3_deg	17.794
r_dihedral_angle_1_deg	7.079
r_scangle_it	3.092
r_scbond_it	1.854
r_angle_refined_deg	1.727
r_mcangle_it	1.233
r_mcbond_it	0.712
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.522
r_dihedral_angle_4_deg	21.808
r_dihedral_angle_3_deg	17.794
r_dihedral_angle_1_deg	7.079
r_scangle_it	3.092
r_scbond_it	1.854
r_angle_refined_deg	1.727
r_mcangle_it	1.233
r_mcbond_it	0.712
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.239
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.1
r_metal_ion_refined	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	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.