PDB-26za: Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rho...

ID or keywords:

Entry

Database: PDB / ID: 26za

Title

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

Components

N-carbamoylsarcosine amidohydrolase

Keywords

HYDROLASE / Cysteine hydrolase

Function / homology

: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / S-1,2-PROPANEDIOL / N-carbamoylsarcosine amidohydrolase

Function and homology information

Biological species

Rhodococcus opacus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Aggarwal, S. / Singh, S. / Aggarwal, D. / Sharma, A.K. / Kumar, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Cysteine-dependent hydrolases (CsdH) from Rhodococcus opacus
Authors: Aggarwal, S. / Singh, S. / Jangid, K. / Aggarwal, D. / Sharma, A.K. / Kumar, P.

History

Deposition	May 21, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 10, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	26za.cif.gz	763.4 KB	Display	PDBx/mmCIF format
PDB format	pdb26za.ent.gz	535.2 KB	Display	PDB format
PDBx/mmJSON format	26za.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/6z/26za ftp://data.pdbj.org/pub/pdb/validation_reports/6z/26za	HTTPS FTP

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Related structure data

Related structure data	26stC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: N-carbamoylsarcosine amidohydrolase

B: N-carbamoylsarcosine amidohydrolase

C: N-carbamoylsarcosine amidohydrolase

D: N-carbamoylsarcosine amidohydrolase

hetero molecules

95.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-carbamoylsarcosine amidohydrolase

hetero molecules

defined by author
Evidence: gel filtration
23.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N-carbamoylsarcosine amidohydrolase

hetero molecules

defined by author
23.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: N-carbamoylsarcosine amidohydrolase

hetero molecules

defined by author
23.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: N-carbamoylsarcosine amidohydrolase

defined by author
23.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.708, 137.45, 190.309
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	PRO	PRO	2 - 218	2 - 218
2	1	1	SER	SER	PRO	PRO	2 - 218	2 - 218
3	2	2	SER	SER	PRO	PRO	2 - 218	2 - 218
4	2	2	SER	SER	PRO	PRO	2 - 218	2 - 218
5	3	3	ALA	ALA	VAL	VAL	8 - 217	8 - 217
6	3	3	ALA	ALA	VAL	VAL	8 - 217	8 - 217
7	4	4	SER	SER	PRO	PRO	2 - 218	2 - 218
8	4	4	SER	SER	PRO	PRO	2 - 218	2 - 218
9	5	5	ALA	ALA	VAL	VAL	8 - 217	8 - 217
10	5	5	ALA	ALA	VAL	VAL	8 - 217	8 - 217
11	6	6	ALA	ALA	VAL	VAL	8 - 217	8 - 217
12	6	6	ALA	ALA	VAL	VAL	8 - 217	8 - 217

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	N-carbamoylsarcosine amidohydrolase Mass: 23791.885 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: O4328_29535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0ABT4NK74
#2: Chemical	ChemComp-PGO / S-1,2-PROPANEDIOL Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium malonate pH7.0 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 27, 2026
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2.8→28.542 Å / Num. obs: 20682 / % possible obs: 99.61 % / Redundancy: 20.9 % / CC_1/2: 0.994 / Net I/σ(I): 38.3
Reflection shell	Resolution: 2.8→2.9 Å / Num. unique obs: 2038 / CC_1/2: 0.977

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrysalisPro		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.8→28.542 Å / Cor.coef. F_o:F_c: 0.88 / Cor.coef. F_o:F_c free: 0.856 / SU B: 41.466 / SU ML: 0.374 / Cross valid method: NONE / ESU R Free: 0.469
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2836	1044	5.054 %
R_work	0.2423	19614	-
all	0.244	-	-
obs	-	20658	99.643 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 53.426 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.611 Å²	-0 Å²	0 Å²
2-	-	-4.274 Å²	0 Å²
3-	-	-	5.885 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→28.542 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6548	0	15	29	6592

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	6668
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6402
X-RAY DIFFRACTION	r_angle_refined_deg	1.715	1.814	9058
X-RAY DIFFRACTION	r_angle_other_deg	0.635	1.75	14692
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.113	5	858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.24	5	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.275	10	1080
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.875	10	284
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1071
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7946
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1510
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	1417
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	6041
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3310
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	3609
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	165
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.016	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.136	0.2	57
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	268
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.276	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.599	1.879	3444
X-RAY DIFFRACTION	r_mcbond_other	1.599	1.879	3444
X-RAY DIFFRACTION	r_mcangle_it	2.762	3.375	4298
X-RAY DIFFRACTION	r_mcangle_other	2.762	3.375	4299
X-RAY DIFFRACTION	r_scbond_it	1.335	1.952	3224
X-RAY DIFFRACTION	r_scbond_other	1.335	1.952	3225
X-RAY DIFFRACTION	r_scangle_it	2.344	3.566	4760
X-RAY DIFFRACTION	r_scangle_other	2.344	3.566	4761
X-RAY DIFFRACTION	r_lrange_it	4.429	18.396	7356
X-RAY DIFFRACTION	r_lrange_other	4.428	18.396	7355
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.059	0.05	6637
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	6632
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.079	0.05	6275
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	6647
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	6286
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.073	0.05	6328

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05945	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.05945	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06657	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06657	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.079	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.079	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0646	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0646	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07913	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07913	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07323	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07323	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.872	0.368	66	0.326	1409	X-RAY DIFFRACTION	99.2598
2.872-2.95	0.357	66	0.32	1388	X-RAY DIFFRACTION	99.9313
2.95-3.034	0.355	78	0.279	1348	X-RAY DIFFRACTION	99.7901
3.034-3.127	0.331	67	0.268	1323	X-RAY DIFFRACTION	100
3.127-3.228	0.303	77	0.242	1234	X-RAY DIFFRACTION	99.8477
3.228-3.34	0.325	61	0.287	1254	X-RAY DIFFRACTION	99.924
3.34-3.464	0.289	55	0.271	1200	X-RAY DIFFRACTION	99.8409
3.464-3.603	0.328	61	0.282	1150	X-RAY DIFFRACTION	100
3.603-3.761	0.268	54	0.26	1101	X-RAY DIFFRACTION	99.9135
3.761-3.941	0.288	69	0.236	1051	X-RAY DIFFRACTION	100
3.941-4.149	0.3	46	0.262	1016	X-RAY DIFFRACTION	99.9059
4.149-4.395	0.287	62	0.239	944	X-RAY DIFFRACTION	99.9007
4.395-4.691	0.236	46	0.217	911	X-RAY DIFFRACTION	100
4.691-5.055	0.248	57	0.214	838	X-RAY DIFFRACTION	99.8884
5.055-5.521	0.284	29	0.201	793	X-RAY DIFFRACTION	99.8785
5.521-6.144	0.289	39	0.204	721	X-RAY DIFFRACTION	99.7375
6.144-7.04	0.287	44	0.194	634	X-RAY DIFFRACTION	100
7.04-8.494	0.153	28	0.153	561	X-RAY DIFFRACTION	99.8305

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.0712	-0.0371	0.2417	4.4688	-0.1657	1.8379	0.0777	-0.0994	0.3569	0.1397	-0.0439	-0.2835	-0.2293	0.0565	-0.0338	0.0357	-0.0131	0.0096	0.1454	-0.0376	0.0667	24.0234	16.5305	5.8203
2	2.5414	0.592	0.2952	3.2934	-0.6721	1.2287	0.1273	0.1473	0.3401	-0.1967	-0.0025	0.5076	-0.1488	-0.0683	-0.1248	0.0687	0.0293	-0.0001	0.1923	-0.0049	0.1114	5.1697	14.7084	-9.6163
3	2.4101	-0.5816	0.6195	2.6417	0.1825	2.8569	-0.0796	-0.2248	-0.5009	0.1247	0.0188	-0.136	0.3893	0.1748	0.0608	0.4299	0.0447	0.1098	0.5637	0.0445	0.1654	-22.8547	16.2687	-38.7121
4	0.7487	-0.4824	-0.5267	5.1622	-1.1863	1.8309	0.1532	-0.0794	0.5245	0.3287	-0.0219	0.066	-0.4214	0.211	-0.1313	0.5239	0.0138	0.1761	0.5381	-0.0446	0.5634	-38.6528	47.3487	-37.3494

Refinement TLS group

Selection: ALL

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