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

ID or keywords:

Entry

Database: PDB / ID: 26st

Title

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

Components

N-carbamoylsarcosine amidohydrolase

Keywords

HYDROLASE / Cysteine hydrolase

Function / homology

: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / PHTHALIC ACID / N-carbamoylsarcosine amidohydrolase

Function and homology information

Biological species

Rhodococcus opacus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Aggarwal, S. / Singh, S. / Jangid, K. / 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 13, 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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PDBx/mmCIF format	26st.cif.gz	762.8 KB	Display	PDBx/mmCIF format
PDB format	pdb26st.ent.gz	535.9 KB	Display	PDB format
PDBx/mmJSON format	26st.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/6s/26st ftp://data.pdbj.org/pub/pdb/validation_reports/6s/26st	HTTPS FTP

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Related structure data

Related structure data	26zaC 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

95.5 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
24 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N-carbamoylsarcosine amidohydrolase

hetero molecules

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

3

C: N-carbamoylsarcosine amidohydrolase

defined by author
23.8 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)	62.285, 136.51, 188.382
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	LEU	LEU	VAL	VAL	4 - 217	4 - 217
4	2	2	LEU	LEU	VAL	VAL	4 - 217	4 - 217
5	3	3	ALA	ALA	VAL	VAL	6 - 217	6 - 217
6	3	3	ALA	ALA	VAL	VAL	6 - 217	6 - 217
7	4	4	LEU	LEU	VAL	VAL	4 - 217	4 - 217
8	4	4	LEU	LEU	VAL	VAL	4 - 217	4 - 217
9	5	5	ALA	ALA	VAL	VAL	6 - 217	6 - 217
10	5	5	ALA	ALA	VAL	VAL	6 - 217	6 - 217
11	6	6	ALA	ALA	VAL	VAL	6 - 217	6 - 217
12	6	6	ALA	ALA	VAL	VAL	6 - 217	6 - 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-PHT / PHTHALIC ACID Mass: 166.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₈H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.1 Å³/Da / Density % sol: 41.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium malonate pH 7.0 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: Mar 4, 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: 2.9→28.524 Å / Num. obs: 18141 / % possible obs: 99.29 % / Redundancy: 6.5 % / CC_1/2: 0.994 / Net I/σ(I): 22.19
Reflection shell	Resolution: 2.9→3.004 Å / Num. unique obs: 1773 / CC_1/2: 0.931

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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: 2.9→28.524 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.869 / SU B: 31.3 / SU ML: 0.28 / Cross valid method: NONE / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2468	906	4.996 %
R_work	0.1917	17230	-
all	0.194	-	-
obs	-	18136	99.354 %

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: 51.981 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.351 Å²	-0 Å²	-0 Å²
2-	-	5.025 Å²	0 Å²
3-	-	-	-1.674 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→28.524 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6547	0	24	26	6597

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	6677
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6392
X-RAY DIFFRACTION	r_angle_refined_deg	1.58	1.813	9074
X-RAY DIFFRACTION	r_angle_other_deg	0.557	1.75	14663
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.035	5	858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.545	5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.851	10	1079
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.858	10	284
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1068
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7977
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1517
X-RAY DIFFRACTION	r_nbd_refined	0.248	0.2	1373
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	6007
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	3457
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	3588
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.208	0.2	136
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.369	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.167	0.2	72
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	227
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.232	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.775	2.248	3444
X-RAY DIFFRACTION	r_mcbond_other	1.775	2.248	3444
X-RAY DIFFRACTION	r_mcangle_it	3.017	4.032	4298
X-RAY DIFFRACTION	r_mcangle_other	3.017	4.033	4299
X-RAY DIFFRACTION	r_scbond_it	1.789	2.44	3233
X-RAY DIFFRACTION	r_scbond_other	1.788	2.44	3234
X-RAY DIFFRACTION	r_scangle_it	3.083	4.409	4776
X-RAY DIFFRACTION	r_scangle_other	3.082	4.41	4777
X-RAY DIFFRACTION	r_lrange_it	5.392	22.886	7406
X-RAY DIFFRACTION	r_lrange_other	5.391	22.843	7405
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.064	0.05	6760
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.069	0.05	6644
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.072	0.05	6519
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	6647
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.063	0.05	6552
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.059	0.05	6545

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	0.0643	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0643	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06888	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06888	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07214	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07214	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06345	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06345	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06316	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06316	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05931	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.05931	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 (%)
2.9-2.975	0.292	67	0.211	1254	X-RAY DIFFRACTION	98.9513
2.975-3.057	0.258	70	0.225	1198	X-RAY DIFFRACTION	100
3.057-3.145	0.287	53	0.219	1226	X-RAY DIFFRACTION	100
3.145-3.242	0.226	63	0.201	1148	X-RAY DIFFRACTION	100
3.242-3.348	0.283	57	0.221	1118	X-RAY DIFFRACTION	100
3.348-3.466	0.314	60	0.234	1113	X-RAY DIFFRACTION	100
3.466-3.597	0.245	46	0.217	1058	X-RAY DIFFRACTION	100
3.597-3.743	0.331	61	0.245	1022	X-RAY DIFFRACTION	100
3.743-3.91	0.23	52	0.198	972	X-RAY DIFFRACTION	99.8051
3.91-4.101	0.267	54	0.193	935	X-RAY DIFFRACTION	100
4.101-4.322	0.249	47	0.175	890	X-RAY DIFFRACTION	99.8934
4.322-4.584	0.245	40	0.163	846	X-RAY DIFFRACTION	99.5506
4.584-4.901	0.225	51	0.162	794	X-RAY DIFFRACTION	99.8818
4.901-5.293	0.184	35	0.161	762	X-RAY DIFFRACTION	99.8747
5.293-5.798	0.194	39	0.16	690	X-RAY DIFFRACTION	99.5902
5.798-6.481	0.22	26	0.182	626	X-RAY DIFFRACTION	99.542
6.481-7.483	0.257	35	0.188	554	X-RAY DIFFRACTION	99.1582
7.483-9.161	0.15	17	0.13	476	X-RAY DIFFRACTION	97.4308

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	2.2534	0.1509	-0.1564	3.4158	-0.068	2.4155	0.0533	0.1539	-0.3053	-0.1323	-0.0366	-0.1574	0.2466	0.1188	-0.0167	0.0335	0.0288	-0.0073	0.1025	-0.0326	0.0491	-7.1745	-16.4314	-5.8947
2	2.9898	-0.7648	0.089	3.2714	-0.4929	1.158	0.1724	-0.1126	-0.2284	0.1353	-0.0839	0.4481	0.1904	-0.1079	-0.0885	0.0628	-0.0293	0.0068	0.1158	0.016	0.0712	-25.9668	-14.6129	9.6606
3	2.5261	0.4984	0.0726	3.2387	0.7352	3.5298	-0.1054	0.2168	0.4436	-0.1154	-0.021	0.0645	-0.3358	0.2288	0.1264	0.2575	-0.0491	0.0567	0.3597	0.0651	0.1174	-53.7204	-16.4517	38.1834
4	2.0947	0.0562	0.5496	4.3357	-0.4425	2.2315	0.2042	0.1351	-0.7216	-0.2882	-0.0733	0.0616	0.5144	0.0993	-0.1309	0.5138	-0.0013	-0.2084	0.4304	-0.0457	0.3333	-69.5955	-47.4401	36.9366

Refinement TLS group

Selection: ALL

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