4LRS | pdb_00004lrs

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NVM	PDB ENTRY 1NVM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	26-34% PEG 4000 or 3350, 0.1 M Tris, 0.2 M Li2SO4, 0.005M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.88	α = 90
b = 92.21	β = 100.59
c = 56.48	γ = 90

Symmetry
Space Group	C 1 2 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		2011-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

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	1.55	43.35	97.6	0.059	13.68	3.98		424737		3

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	1.55	1.59	85.2		0.365	3.06	3.01

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 1NVM	1.55	25	3	424737	101394	5337	97.7	0.166	0.164	0.19	0.2	0.21	RANDOM	12.42

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]
-0.66		1.03	-1.1		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.653
r_sphericity_free	19.495
r_dihedral_angle_4_deg	12.704
r_dihedral_angle_3_deg	12.446
r_dihedral_angle_1_deg	5.561
r_sphericity_bonded	5.316
r_rigid_bond_restr	2.673
r_angle_refined_deg	1.461
r_chiral_restr	0.099
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4682
Nucleic Acid Atoms
Solvent Atoms	565
Heterogen Atoms	145

Software

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