5J23 | pdb_00005j23

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition #20 (1.1 M Malonic acid, 0.072 M Succinic acid, 0.15M Ammonium dihydrogen citrate, 0.18 M DL-Malic Acid, 0.096 M Ammonium tartrate, 0.24 M Sodium acetate anhydrous, 0.3 M Sodium formate, pH=7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.822	α = 90
b = 175.822	β = 90
c = 136.839	γ = 120

Symmetry
Space Group	H 3

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	2014-11-06	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)	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	2.3	50	100	0.077	0.077	7.5	3.9		70083		-3	45.8

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	2.3	2.34	100		0.662	1.8	3.9

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	4Z0P	2.3	36.67	66631	3434	99.91	0.1475	0.1464	0.15	0.169	0.18	RANDOM	46.78

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]
-8.99			-8.99		17.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.241
r_dihedral_angle_4_deg	20.554
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	5.437
r_mcangle_it	2.02
r_angle_refined_deg	1.491
r_mcbond_it	1.293
r_mcbond_other	1.281
r_angle_other_deg	1.21
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.241
r_dihedral_angle_4_deg	20.554
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	5.437
r_mcangle_it	2.02
r_angle_refined_deg	1.491
r_mcbond_it	1.293
r_mcbond_other	1.281
r_angle_other_deg	1.21
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9454
Nucleic Acid Atoms
Solvent Atoms	603
Heterogen Atoms	179

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	data scaling
HKL-3000	data reduction
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.