9DWO | pdb_00009dwo

Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DTL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	292	Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate; Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 25% (w/v) PEG 1500; Cryo: Reservoir

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.678	α = 90
b = 66.953	β = 90
c = 87.688	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12723	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	1.5	30	98.6	0.14	0.14	0.146	0.04	0.998	18.7	12.5		44360		-3	12.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	98.1		0.356	0.607	2.4	12.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.5	28.84	41929	2200	98.56	0.17648	0.17463	0.1756	0.21209	0.2132	RANDOM	16.349

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]
0.18			-1.12		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	8.938
r_long_range_B_refined	6.054
r_long_range_B_other	5.846
r_dihedral_angle_1_deg	4.667
r_scangle_other	3.702
r_scbond_other	2.357
r_scbond_it	2.356
r_dihedral_angle_2_deg	1.887
r_mcangle_other	1.576
r_mcangle_it	1.57
r_angle_refined_deg	1.488
r_mcbond_it	1.047
r_mcbond_other	1.047
r_angle_other_deg	0.478
r_chiral_restr	0.078
r_gen_planes_refined	0.02
r_gen_planes_other	0.016
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2320
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing