9T0W | pdb_00009t0w

Crystal structure of the Mycobacterium tuberculosis histidinol-phosphate aminotransferase HisC in complex with the adduct PLP-BVL3572S

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M ammonium sulfate, 0.01 M Tris, pH 7.0, 0.075 M NaCl, 15% (w/v) PEG MME 5000, 0.05 M MES, 0.025 mM PLP, TEMPERATURE 293K, VAPOR DIFFUSION, crystals were soaked in crystallization solution supplemented with BVL3572S for 1 second and cryoprotected with 20% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.603	α = 90
b = 101.59	β = 90
c = 115.53	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	PIXEL	DECTRIS EIGER X 9M		2021-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.737	58.42	100	0.167	0.181	0.068	0.995	7.5	7.1		82707

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.737	1.767	100		2.445	2.668	1.087	0.343	0.8	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.74	58.42	82395	4098	99.616	0.195	0.1935	0.2035	0.2306	0.2368	29.301

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]
-0.04			0.054		-0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	27.691
r_dihedral_angle_6_deg	16.595
r_dihedral_angle_3_deg	13.109
r_dihedral_angle_2_deg	12.968
r_lrange_other	8.283
r_lrange_it	8.281
r_scangle_it	7.122
r_scangle_other	7.121
r_dihedral_angle_1_deg	6.777
r_mcangle_it	5.421
r_mcangle_other	5.42
r_scbond_it	4.975
r_scbond_other	4.974
r_mcbond_it	3.904
r_mcbond_other	3.904
r_angle_refined_deg	2.199
r_angle_other_deg	0.723
r_symmetry_xyhbond_nbd_refined	0.288
r_symmetry_nbd_refined	0.266
r_nbd_other	0.229
r_nbd_refined	0.215
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.106
r_ncsr_local_group_1	0.086
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5496
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
autoPROC	data reduction
XDS	data scaling
Aimless	data scaling
MOLREP	phasing