8ZJ5 | pdb_00008zj5

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	295	0.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.041	α = 90
b = 94.469	β = 90
c = 167.425	γ = 90

Symmetry
Space Group	P 2 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	RIGAKU HyPix-6000HE		2022-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	2.8	24.46	99.6	0.23	0.248	0.97	6.8	12.8		34601

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	2.8	2.94	100		0.814	0.89	0.759	1.9	10.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	23.721	34564	1768	99.476	0.262	0.2595	0.261	0.3031	0.3056	21.633

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]
-1.942			2.397		-0.455

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.835
r_dihedral_angle_6_deg	13.737
r_dihedral_angle_2_deg	11.038
r_dihedral_angle_1_deg	6.409
r_lrange_it	5.38
r_lrange_other	5.287
r_rigid_bond_restr	2.462
r_angle_refined_deg	1.372
r_mcangle_it	0.927
r_mcangle_other	0.927
r_scangle_it	0.858
r_scangle_other	0.858
r_mcbond_it	0.54
r_mcbond_other	0.54
r_scbond_it	0.501
r_scbond_other	0.501
r_angle_other_deg	0.462
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.213
r_symmetry_nbd_other	0.2
r_nbd_other	0.197
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_other	0.125
r_symmetry_nbd_refined	0.119
r_ncsr_local_group_3	0.095
r_ncsr_local_group_5	0.09
r_ncsr_local_group_4	0.089
r_ncsr_local_group_2	0.083
r_ncsr_local_group_6	0.082
r_ncsr_local_group_1	0.081
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9153
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing