3ZZI | pdb_00003zzi

Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZZF	PDB ENTRY 3ZZF FOR ONE DOMAIN, AND AN INCOMPLETE TRACING FROM OTHER CRYSTAL OF THE SAME PRESENT PROTEIN FOR THE SECOND DOMAIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH 7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED WITH 40 MM NAG, WAS CRYSTALLIZED IN PRESENCE OF 0.2 M AMMONIUM CITRATE PH 7.0 AND 12 % PEG3350 AS CRYSTALLIZATION SOLUTION, IN SITTING DROPS AT 4C. CRYOBUFFER SOLUTION WAS THAT OF CRYSTALLIZATION WITH PEG3350 ENRICHED TO 40 %.

Crystal Properties
Matthews coefficient	Solvent content
2.64	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.24	α = 75.77
b = 111.29	β = 89.29
c = 113.14	γ = 69.12

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 CCD		2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	3.8	109	96.3	0.057	10.5	2.4		39773		1.5

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	3.8	4.01	96.3		0.455	1.5	2.4

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	PDB ENTRY 3ZZF FOR ONE DOMAIN, AND AN INCOMPLETE TRACING FROM OTHER CRYSTAL OF THE SAME PRESENT PROTEIN FOR THE SECOND DOMAIN	3.8	109.11	37381	1985	95.33	0.19914	0.19725	0.2	0.23592	0.25	RANDOM	127.643

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]
-0.52	1.34	-1.42	-0.06	0.68	-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.199
r_dihedral_angle_3_deg	22.196
r_dihedral_angle_4_deg	15.305
r_dihedral_angle_1_deg	8.1
r_angle_other_deg	1.831
r_angle_refined_deg	1.793
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_bond_other_d	0.011
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27248
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing