2A9K | pdb_00002a9k

Crystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a bacterial exoenzyme

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G24	1G24, 1UAD
experimental model	PDB	1UAD	1G24, 1UAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2 M ammonium citrate pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.26	α = 90
b = 113.85	β = 106.4
c = 56.31	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	IMAGE PLATE	MARRESEARCH	OSMIC BLUE	2004-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.73	20	90.2	0.049	13.2	2.9	40078	40078		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.83	62.6		0.239	3.6

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	1G24, 1UAD	1.73	19.03	40077	38073	2004	100	0.18834	0.18834	0.18648	0.19	0.22465	0.23	RANDOM	21.023

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]
-0.79		0.42	-0.42		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.09
r_dihedral_angle_4_deg	16.503
r_dihedral_angle_3_deg	13.677
r_dihedral_angle_1_deg	5.202
r_scangle_it	2.08
r_scbond_it	1.291
r_angle_refined_deg	1.11
r_mcangle_it	0.816
r_mcbond_it	0.485
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.09
r_dihedral_angle_4_deg	16.503
r_dihedral_angle_3_deg	13.677
r_dihedral_angle_1_deg	5.202
r_scangle_it	2.08
r_scbond_it	1.291
r_angle_refined_deg	1.11
r_mcangle_it	0.816
r_mcbond_it	0.485
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.105
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2995
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	73

Software

Software
Software Name	Purpose
MAR345	data collection
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
XDS	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.