7N1L | pdb_00007n1l

Crystal Structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis biovar Abortus 2308

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5F47	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	6BVC	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	5HMN	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	2FE7	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	3I9S	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	3FYN	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	2EUI	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	1QSM	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	3T9Y	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	1Z4E	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	1S3Z	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	2R1I	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	3JVN	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	2DXQ	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	5T7D	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	3D8P	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	4E04	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	4EVY	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4
experimental model	PDB	1MK4	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	287	RigakuReagents JCSG+ screen, condition G1: 30% (V/V) Jeffamine ED-2003, 100mM HEPES free acid / sodium hydroxide pH 7.0: BrabA.17502.a.A1.PS01129 at 26mg/ml: tray 236060 G1: cryo: 20% EG: puck kzs9-7.

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.02	α = 87.121
b = 114.9	β = 76.271
c = 122	γ = 73.142

Symmetry
Space Group	P 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	ADSC QUANTUM 315r		2012-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97742	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	98.4	0.077	0.09	0.998	14.05	3.862		147858			42.519

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	97.6		0.537	0.623	0.842	2.62	3.878

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4	2.3	48.73	1.98	147834	1756	98.4	0.2094	0.209	0.2087	0.2484	0.2482	0	52.25

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
f_dihedral_angle_d	13.3442
f_angle_d	0.8934
f_chiral_restr	0.0562
f_plane_restr	0.009
f_bond_d	0.0072

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17210
Nucleic Acid Atoms
Solvent Atoms	842
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
PHASER	phasing
Coot	model building
BUCCANEER	model building