2AAJ | pdb_00002aaj

Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		wildtype MSAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	2.8 M Li(CH3COO), 0.7 M (NH4)2SO4, and 100 mM sodium citrate buffer (pH 5.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.152	α = 90
b = 110.152	β = 90
c = 110.152	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	MARRESEARCH		2003-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.74	29.4	99.4	0.129	9.2	12.4	12097	11976		2	38.1

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	2.74	2.86	98.7		0.391			1188

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	wildtype MSAD	2.74	29.4	11328	11251	623	99.32	0.1641	0.1641	0.1614	0.17	0.2133	0.17	RANDOM	31.56

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.792
r_sphericity_free	3.599
r_scangle_it	3.292
r_scbond_it	1.989
r_angle_refined_deg	1.923
r_mcangle_it	1.417
r_rigid_bond_restr	1.113
r_sphericity_bonded	1.105
r_mcbond_it	0.789
r_symmetry_hbond_refined	0.215

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.792
r_sphericity_free	3.599
r_scangle_it	3.292
r_scbond_it	1.989
r_angle_refined_deg	1.923
r_mcangle_it	1.417
r_rigid_bond_restr	1.113
r_sphericity_bonded	1.105
r_mcbond_it	0.789
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.122
r_bond_refined_d	0.021
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1974
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

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.