3LX3 | pdb_00003lx3

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in complex with xanthopterin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A0S	2a0s, A chain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	298	2 ul 5 mg/ml protein (refolded in SGPP buffer + 0.01 mM Zn2+) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 10 mM MgCl2, 1 mM TCEP, 2 mM xanthopterin; cryoprotected by 3 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.358	α = 90
b = 131.358	β = 90
c = 73.577	γ = 120

Symmetry
Space Group	H 3 2

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 325 mm CCD		2009-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

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	1.55	50	99.6	0.057	12.8	9		35343		4	28

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)
	1.55	1.61	96.3		0.762	1.8	6.5	3414

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2a0s, A chain	1.55	37.12	35342	1835	99.55	0.15	0.149	0.1604	0.167	0.1767	RANDOM	25.948

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]
-0.95	-0.47		-0.95		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.795
r_dihedral_angle_4_deg	20.364
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	6.475
r_scangle_it	6.269
r_scbond_it	3.97
r_mcangle_it	2.871
r_mcbond_it	1.783
r_angle_refined_deg	1.676
r_angle_other_deg	0.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.795
r_dihedral_angle_4_deg	20.364
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	6.475
r_scangle_it	6.269
r_scbond_it	3.97
r_mcangle_it	2.871
r_mcbond_it	1.783
r_angle_refined_deg	1.676
r_angle_other_deg	0.939
r_mcbond_other	0.605
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1396
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
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.