3TNL | pdb_00003tnl

1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and NAD.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPD	pdb entry 1NPD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3), 1mM Shikimate; Screen: PEG's (D2), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 4000. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.851	α = 90
b = 82.878	β = 90.03
c = 101.26	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	Beryllium lenses	2011-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.45	30	96.7	0.055	20.6	3.8	203043	203043		-3	17.9

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	1.45	1.48	89.4		0.34	3.1	3.4	9339

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 (All)	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 1NPD	1.45	29.31	192681	192681	10155	96.68	0.15011	0.15011	0.14871	0.16	0.17645	0.18	RANDOM	15.508

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]
-1.26		1.23	1.72		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.385
r_dihedral_angle_4_deg	12.325
r_dihedral_angle_3_deg	9.119
r_scangle_it	4.708
r_dihedral_angle_1_deg	3.872
r_scbond_it	2.922
r_mcangle_it	1.761
r_angle_refined_deg	1.607
r_mcbond_it	1.079
r_angle_other_deg	0.898

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.385
r_dihedral_angle_4_deg	12.325
r_dihedral_angle_3_deg	9.119
r_scangle_it	4.708
r_dihedral_angle_1_deg	3.872
r_scbond_it	2.922
r_mcangle_it	1.761
r_angle_refined_deg	1.607
r_mcbond_it	1.079
r_angle_other_deg	0.898
r_mcbond_other	0.382
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8944
Nucleic Acid Atoms
Solvent Atoms	1907
Heterogen Atoms	204

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
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.