PDB-4h0c: Crystal structure of phospholipase/Carboxylesterase from Dyadobac...

ID or keywords:

Entry

Database: PDB / ID: 4h0c

Title

Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053

Components

Phospholipase/Carboxylesterase

Keywords

HYDROLASE / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / phospholipase/Carboxylesterase

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Dyadobacter fermentans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.62 Å

Authors

Chang, C. / Holowicki, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053
Authors: Chang, C. / Holowicki, J. / Clancy, S. / Joachimiak, A.

History

Deposition	Sep 7, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4h0c.cif.gz	182.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4h0c.ent.gz	155.7 KB	Display	PDB format
PDBx/mmJSON format	4h0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h0/4h0c ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h0c	HTTPS FTP

-
Related structure data

Similar structure data	2r8b-1 3p2h-d 2wl1-d 5e1o-2 3ou2-d 6ogo-3 2nv0-2 6tya-d 1qy6-d 1ajo-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC103406

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phospholipase/Carboxylesterase

B: Phospholipase/Carboxylesterase

hetero molecules

46.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phospholipase/Carboxylesterase

hetero molecules

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

2

B: Phospholipase/Carboxylesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.157, 40.251, 67.256
Angle α, β, γ (deg.)	72.770, 78.370, 76.090
Int Tables number	1
Space group name H-M	P1

#1: Protein	Phospholipase/Carboxylesterase Mass: 22862.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dyadobacter fermentans (bacteria) / Strain: DSM 18053 / Gene: Dfer_0355 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C6VYE5
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.64 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M tri sodium citrate, 20% PEG4000, 5% iso-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2012
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.62→63.6 Å / Num. all: 49246 / Num. obs: 47679 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 96.8 % / R_merge(I) obs: 0.089 / Net I/σ(I): 22
Reflection shell	Resolution: 1.62→1.63 Å / Redundancy: 3 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.15 / Num. unique all: 1166 / % possible all: 94

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
ARP/wARP		model building
RESOLVE		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.62→63.6 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.584 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.091
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.194	2412	5.1 %	RANDOM
R_work	0.1362	-	-	-
all	0.1391	47507	-	-
obs	0.1391	47507	96.05 %	-

Solvent computation

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

Displacement parameters

B_iso max: 67.88 Å² / B_iso mean: 20.7163 Å² / B_iso min: 9.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0.2 Å²	-1.17 Å²
2-	-	-0.68 Å²	-0.49 Å²
3-	-	-	1.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→63.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3174	0	34	249	3457

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	3368
X-RAY DIFFRACTION	r_angle_refined_deg	1.293	1.967	4595
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.886	5	437
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.469	25.319	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.22	15	551
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.612	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	520
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2589
X-RAY DIFFRACTION	r_rigid_bond_restr	2.361	3	3368
X-RAY DIFFRACTION	r_sphericity_free	29.274	5	87
X-RAY DIFFRACTION	r_sphericity_bonded	13.473	5	3461

LS refinement shell

Resolution: 1.617→1.659 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.273	172	-
R_work	0.204	3089	-
all	-	3261	-
obs	-	3261	89.17 %

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	0.3441	-0.2993	0.4899	1.0196	-1.0552	1.3007	0.0123	-0.0025	-0.0163	-0.0068	0.0233	0.0243	0.0182	-0.0352	-0.0356	0.0123	0.0028	0.0003	0.0212	0.006	0.0025	8.715	37.7285	52.0292
2	0.0094	0.0196	-0.0184	0.1096	-0.1656	0.2735	0.0058	0.0022	-0.0009	0.0009	0.0042	0.0043	0.0063	0.001	-0.01	0.012	0.0025	0.0023	0.0235	0.0079	0.0075	19.1477	32.0813	62.998
3	0.605	-0.2048	0.0221	0.1407	-0.0628	0.0443	0.0082	0.0216	-0.0123	-0.0017	-0.0166	-0.0048	-0.0001	0.0117	0.0084	0.0131	0.0025	0.0038	0.0228	0.0089	0.0057	27.0022	29.1019	61.5555
4	0.0058	0.0141	-0.0186	0.0346	-0.0457	0.0615	-0.0003	0.0013	0.0013	0.0008	0.0038	0.0041	0.0009	-0.0011	-0.0035	0.0118	0.004	0.0032	0.0238	0.0089	0.0081	16.328	41.6184	50.7468
5	0.0151	-0.071	0.1038	0.4008	-0.6549	1.2887	0.0031	-0.0027	-0.0045	0.0009	0.0167	0.0144	0.0003	-0.0216	-0.0198	0.0112	0.0035	0.0019	0.0212	0.0069	0.0079	11.1743	44.0262	56.7343
6	1.546	0.478	-0.6286	0.328	-0.2771	0.392	0.0327	-0.0365	0.0097	0.0265	-0.0156	0.0068	-0.0092	0.0159	-0.0171	0.0131	0.0035	0.0025	0.0196	0.0065	0.0043	17.8581	38.9377	72.5881
7	0.0142	-0.0061	0.0418	0.0405	-0.0143	0.124	0.0002	0.0001	0.0007	0.002	-0.0014	-0.0009	-0.002	-0.002	0.0012	0.0112	0.0028	0.0028	0.0216	0.0081	0.008	22.3997	45.9091	58.5769
8	2.1163	-0.097	-3.521	1.0555	0.6165	6.7597	0.0865	-0.005	0.0297	-0.0515	-0.0046	-0.0027	-0.198	-0.0155	-0.0819	0.0094	0.0029	0.0024	0.0163	0.0078	0.0057	19.1981	59.0851	54.1617
9	0.0691	-0.0329	-0.0125	0.0168	0.006	0.203	-0.0031	-0.0052	0.0046	-0.0001	0.0053	-0.0023	0.0066	0.0081	-0.0022	0.0108	-0.0003	0.0026	0.0194	0.0085	0.0074	28.5599	48.8731	58.6595
10	0.2384	-0.0648	-0.0047	0.0192	0.0278	0.5258	0.0059	0.0155	0.0064	-0.0019	-0.0013	-0.0011	-0.0209	0.0161	-0.0046	0.0113	0.0005	0.0021	0.0202	0.0079	0.0061	30.1275	53.7419	57.7771
11	0.0984	0.0247	-0.0344	0.1177	-0.0711	0.653	0.0004	-0.0025	-0.0074	-0.0051	-0.0044	-0.0074	0.0203	0.0275	0.004	0.0077	0.0038	0.0031	0.0229	0.0081	0.006	36.3991	38.9674	57.2437
12	0.3781	-0.4243	-0.6181	0.9794	0.9172	1.1658	0.0287	-0.0087	0.0286	0.0127	0.0137	-0.0509	-0.013	0.0051	-0.0424	0.0101	0.0008	0.0048	0.0251	0.0049	0.0084	39.5219	55.1508	27.6471
13	0.0868	0.0013	-0.1022	0.0388	0.0747	0.2709	-0.0009	0.0008	0.0012	-0.0019	0.0011	0	-0.0013	0.0052	-0.0002	0.0119	0.0043	0.0019	0.0208	0.0087	0.007	41.3795	43.4175	16.9076
14	0.1702	-0.0032	-0.03	0.3974	-0.0884	0.0257	-0.0072	-0.0042	-0.0065	0.0186	0.0037	-0.0093	-0.0012	0.0027	0.0035	0.0129	0.0047	0.0011	0.0255	0.0078	0.0062	42.8406	35.2706	18.6211
15	0.0823	0.0276	-0.0668	0.0929	0.0328	0.0908	0.0155	-0.0048	0.0103	0.005	-0.0042	-0.0006	-0.0124	0.0023	-0.0113	0.0121	0.0048	0.0019	0.025	0.0087	0.0055	33.7664	49.0299	29.4649
16	0.2283	-0.1426	-0.4646	0.1313	0.2626	1.1418	0.0138	-0.0031	0.0158	0.0006	0.0099	-0.0109	-0.0074	0.0051	-0.0237	0.0115	0.0013	0.002	0.0208	0.0083	0.0066	32.1796	54.2848	23.312
17	0.3687	0.314	-0.143	0.8547	-0.4291	0.2257	-0.0023	0.0294	-0.0157	-0.0209	-0.0045	-0.0182	0.0128	-0.0016	0.0069	0.0102	0.0037	0.0041	0.0225	0.007	0.0057	34.367	45.8982	7.6571
18	0.0058	-0.0127	-0.0015	0.031	0.0121	0.0944	0.0013	0.0025	0.0012	0.0008	0.0004	0.001	-0.0009	0.0012	-0.0018	0.0123	0.0023	0.0029	0.0227	0.0088	0.0079	27.6361	43.7009	22.3064
19	0.7969	0.9221	1.4358	1.1029	1.7302	2.7185	0.0965	-0.0984	0.1269	0.1676	-0.1115	0.0471	0.271	-0.1296	0.015	0.0563	0.0357	-0.0532	0.0915	-0.0674	0.3005	15.6859	49.4725	27.0664
20	0.0686	-0.1033	0.0807	0.1613	-0.0828	0.3985	-0.0032	-0.0012	-0.0012	0.0062	0.0024	0.0015	0.008	-0.0105	0.0009	0.0081	0.0005	0.002	0.0205	0.0097	0.0075	23.5019	38.31	22.7746
21	0.0946	0.0024	0.0709	0.1043	-0.0223	0.3013	0.006	-0.0056	-0.0098	0.01	0.0002	0.0035	0.0056	-0.0168	-0.0062	0.0121	0.0019	0.0037	0.0212	0.008	0.0072	18.4229	37.9181	24.0255
22	0.1811	0.0243	-0.172	0.1374	-0.1814	0.5427	-0.004	-0.0012	-0.0163	-0.0067	-0.0014	0.0002	0.021	0.0121	0.0054	0.0103	0.002	0.0028	0.0182	0.0082	0.0077	31.62	28.5688	24.1659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 33
3	X-RAY DIFFRACTION	3	A	34 - 46
4	X-RAY DIFFRACTION	4	A	47 - 69
5	X-RAY DIFFRACTION	5	A	70 - 89
6	X-RAY DIFFRACTION	6	A	90 - 100
7	X-RAY DIFFRACTION	7	A	101 - 135
8	X-RAY DIFFRACTION	8	A	136 - 141
9	X-RAY DIFFRACTION	9	A	142 - 161
10	X-RAY DIFFRACTION	10	A	162 - 182
11	X-RAY DIFFRACTION	11	A	183 - 207
12	X-RAY DIFFRACTION	12	B	-1 - 10
13	X-RAY DIFFRACTION	13	B	11 - 33
14	X-RAY DIFFRACTION	14	B	34 - 46
15	X-RAY DIFFRACTION	15	B	47 - 69
16	X-RAY DIFFRACTION	16	B	70 - 89
17	X-RAY DIFFRACTION	17	B	90 - 100
18	X-RAY DIFFRACTION	18	B	101 - 135
19	X-RAY DIFFRACTION	19	B	136 - 141
20	X-RAY DIFFRACTION	20	B	142 - 161
21	X-RAY DIFFRACTION	21	B	162 - 182
22	X-RAY DIFFRACTION	22	B	183 - 207

-
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