PDB-27cj: Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rho...

ID or keywords:

Entry

Database: PDB / ID: 27cj

Title

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

Components

N-carbamoylsarcosine amidohydrolase

Keywords

HYDROLASE / Cysteine hydrolase

Function / homology

: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / ETHANOL / 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. / Aggarwal, D. / Sharma, A.K. / Kumar, P.

Funding support

India, 1items

Citation

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

History

Deposition	May 26, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 10, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	27cj.cif.gz	400.9 KB	Display	PDBx/mmCIF format
PDB format	pdb27cj.ent.gz	278.2 KB	Display	PDB format
PDBx/mmJSON format	27cj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/7c/27cj ftp://data.pdbj.org/pub/pdb/validation_reports/7c/27cj	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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
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
23.8 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)	62.708, 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	MET	MET	PRO	PRO	1 - 218	1 - 218
2	1	1	MET	MET	PRO	PRO	1 - 218	1 - 218
3	2	2	ALA	ALA	VAL	VAL	3 - 217	3 - 217
4	2	2	ALA	ALA	VAL	VAL	3 - 217	3 - 217
5	3	3	SER	SER	VAL	VAL	2 - 217	2 - 217
6	3	3	SER	SER	VAL	VAL	2 - 217	2 - 217
7	4	4	ALA	ALA	VAL	VAL	3 - 217	3 - 217
8	4	4	ALA	ALA	VAL	VAL	3 - 217	3 - 217
9	5	5	SER	SER	VAL	VAL	2 - 217	2 - 217
10	5	5	SER	SER	VAL	VAL	2 - 217	2 - 217
11	6	6	ALA	ALA	VAL	VAL	3 - 217	3 - 217
12	6	6	ALA	ALA	VAL	VAL	3 - 217	3 - 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.: 1 / Source method: obtained synthetically / Formula: C₈H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium malonate pH 7.0 20%PEG 3350

-
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-3000 / Detector: PIXEL / Date: Apr 16, 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→28.11 Å / Num. obs: 18637 / % possible obs: 99.6 % / Redundancy: 20 % / CC_1/2: 0.994 / Net I/σ(I): 41.45
Reflection shell	Resolution: 2.9→3.004 Å / Num. unique obs: 1830 / CC_1/2: 0.984

-
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→28.11 Å / Cor.coef. F_o:F_c: 0.878 / Cor.coef. F_o:F_c free: 0.855 / SU B: 42 / SU ML: 0.442 / Cross valid method: NONE / ESU R Free: 0.467 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.263	531	2.852 %
R_work	0.2394	18088	-
all	0.24	-	-
obs	-	18619	99.673 %

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: 51.987 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.599 Å²	-0 Å²	0 Å²
2-	-	-3.846 Å²	0 Å²
3-	-	-	5.445 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→28.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6594	0	15	19	6628

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	6716
X-RAY DIFFRACTION	r_angle_refined_deg	1.909	1.813	9125
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.935	5	865
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.368	5	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.882	10	1089
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.937	10	284
X-RAY DIFFRACTION	r_chiral_restr	0.144	0.2	1077
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5044
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	3051
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	4602
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	231
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	232
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	1.235	1.505	3472
X-RAY DIFFRACTION	r_mcangle_it	2.143	2.703	4333
X-RAY DIFFRACTION	r_scbond_it	1.248	1.564	3244
X-RAY DIFFRACTION	r_scangle_it	2.151	2.858	4792
X-RAY DIFFRACTION	r_lrange_it	4.554	16.72	10080
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	6648
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.076	0.05	6522
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.071	0.05	6567
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.077	0.05	6553
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.071	0.05	6604
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.066	0.05	6555

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	0.07733	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07733	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07614	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07614	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07053	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07053	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07679	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07679	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07146	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07146	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06554	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06554	0.05009

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 (%)
2.9-2.974	0.324	21	0.324	1316	X-RAY DIFFRACTION	99.9253
2.974-3.055	0.337	23	0.3	1277	X-RAY DIFFRACTION	99.7698
3.055-3.142	0.251	27	0.251	1273	X-RAY DIFFRACTION	100
3.142-3.238	0.325	26	0.278	1191	X-RAY DIFFRACTION	99.8359
3.238-3.343	0.449	26	0.289	1177	X-RAY DIFFRACTION	99.9169
3.343-3.458	0.255	23	0.255	1158	X-RAY DIFFRACTION	99.8309
3.458-3.587	0.282	23	0.261	1099	X-RAY DIFFRACTION	100
3.587-3.731	0.259	21	0.257	1068	X-RAY DIFFRACTION	99.9083
3.731-3.894	0.263	37	0.234	1004	X-RAY DIFFRACTION	100
3.894-4.08	0.353	26	0.246	974	X-RAY DIFFRACTION	100
4.08-4.296	0.264	35	0.222	926	X-RAY DIFFRACTION	99.7923
4.296-4.55	0.321	32	0.218	889	X-RAY DIFFRACTION	100
4.55-4.855	0.198	36	0.198	832	X-RAY DIFFRACTION	100
4.855-5.232	0.281	28	0.204	778	X-RAY DIFFRACTION	99.8761
5.232-5.712	0.261	29	0.216	714	X-RAY DIFFRACTION	99.8656
5.712-6.354	0.189	17	0.188	667	X-RAY DIFFRACTION	99.7085
6.354-7.278	0.277	37	0.219	566	X-RAY DIFFRACTION	99.8344
7.278-8.772	0.221	26	0.157	506	X-RAY DIFFRACTION	99.8124

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	3.3947	-0.1763	0.516	4.7372	-0.0179	2.0628	0.0351	-0.0777	0.3433	0.1499	-0.0444	-0.2621	-0.2151	0.0654	0.0093	0.0306	-0.0191	0.0038	0.0846	-0.0398	0.0618	23.9755	16.6574	5.7052
2	2.6875	0.8947	0.8349	3.4137	-0.3327	1.6037	0.0813	0.1482	0.3517	-0.2574	0.011	0.529	-0.1117	-0.0136	-0.0924	0.0588	0.0205	-0.0083	0.1199	0.0001	0.1165	5.2529	14.8556	-9.5979
3	3.0708	-0.7665	0.2406	3.0918	0.0907	2.8408	-0.1254	-0.1877	-0.5808	0.1321	0.0089	-0.0365	0.4487	0.1202	0.1165	0.4447	0.0713	0.1138	0.5556	0.0522	0.2448	-22.8385	16.3523	-38.7389
4	1.1225	0.1381	-0.6051	5.0379	-0.9044	2.2794	0.143	-0.1026	0.7073	0.3926	-0.1129	0.1134	-0.4522	0.2867	-0.0301	0.5619	0.0121	0.1963	0.5748	-0.0603	0.582	-38.5927	47.7848	-37.6228

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi