4NS3 | pdb_00004ns3

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	291	0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol)pyruvic acid monosodium salt hydrate, 0.2% w/v D-(+)-Melezitose hydrate, 0.2% w/v cobalamin and 0.02M HEPES sodium pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.855	α = 90
b = 164.855	β = 90
c = 260.242	γ = 120

Symmetry
Space Group	P 31 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	77	CCD	ADSC QUANTUM 315r		2012-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953691	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.38	20.05	99.4				164364

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	2.38	20.049	1.34	163475	8211	99.72	0.1591	0.1566	0.1562	0.2051	0.2033	34.398

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]
-0.25	-0.12		-0.25		0.81

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.604
f_angle_d	1.343
f_chiral_restr	0.115
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24843
Nucleic Acid Atoms
Solvent Atoms	2631
Heterogen Atoms	418

Software

Software
Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
Blu-Ice	data collection

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.