27CJ | pdb_000027cj

Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with dibutylphthalate

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		293	0.1M sodium malonate pH 7.0 20%PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.708	α = 90
b = 137.45	β = 90
c = 190.309	γ = 90

Symmetry
Space Group	C 2 2 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-3000		2026-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.9	28.11	99.6	0.994	41.45	20		18637

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.004			0.984

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	AlphaFold	2.9	28.11	18619	531	99.673	0.24	0.2394	0.2379	0.263	0.2664	51.987

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]
-1.599			-3.846		5.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.882
r_dihedral_angle_6_deg	13.937
r_dihedral_angle_2_deg	10.368
r_dihedral_angle_1_deg	7.935
r_lrange_it	4.554
r_scangle_it	2.151
r_mcangle_it	2.143
r_angle_refined_deg	1.909
r_scbond_it	1.248
r_mcbond_it	1.235
r_nbtor_refined	0.317
r_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.144
r_ncsr_local_group_1	0.077
r_ncsr_local_group_4	0.077
r_ncsr_local_group_2	0.076
r_ncsr_local_group_3	0.071
r_ncsr_local_group_5	0.071
r_ncsr_local_group_6	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6594
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	15

Software

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