PDB-4q82: Crystal Structure of Phospholipase/Carboxylesterase from Haliangi...

ID or keywords:

Entry

Database: PDB / ID: 4q82

Title

Crystal Structure of Phospholipase/Carboxylesterase from Haliangium ochraceum

Components

Phospholipase/Carboxylesterase

Keywords

HYDROLASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-fold

Function / homology

Alpha/Beta hydrolase fold, catalytic domain /

Alpha/Beta hydrolase fold /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta /

FORMIC ACID / Phospholipase/Carboxylesterase

Function and homology information

Biological species

Haliangium ochraceum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.848 Å

Authors

Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Phospholipase/Carboxylesterase from Haliangium ochraceum
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A.

History

Deposition	Apr 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2018	Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4q82.cif.gz	204.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4q82.ent.gz	172.6 KB	Display	PDB format
PDBx/mmJSON format	4q82.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/q8/4q82 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/4q82	HTTPS FTP

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Related structure data

Similar structure data	4nfz-1 3roz-d 6ow7-1 2qq5-d 4nfz-3 1daf-d 1dah-d 1z0k-2 3gy0-d 4na7-d 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC103461

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phospholipase/Carboxylesterase

B: Phospholipase/Carboxylesterase

hetero molecules

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

1

A: Phospholipase/Carboxylesterase

hetero molecules

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

2

B: Phospholipase/Carboxylesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.935, 146.084, 68.720
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-572- HOH
2	1	A-640- HOH

Details

there are two monomers in the asymmetric unit.

#1: Protein	Phospholipase/Carboxylesterase Mass: 29739.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haliangium ochraceum (bacteria) / Strain: DSM 14365 / Gene: Hoch_6203 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: D0LMJ0
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.28 Å³/Da / Density % sol: 62.49 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis Tris Propane pH7.0, 1.8 M magnesium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2013 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. all: 67799 / Num. obs: 67799 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / B_iso Wilson estimate: 18.65 Å² / R_sym value: 0.07 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3307 / R_sym value: 0.64 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
DM		model building
PHENIX	(phenix.refine: 1.9_1678)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.848→41.296 Å / SU ML: 0.13 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.3 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.175	3371	5.06 %	random
R_work	0.153	-	-	-
all	0.154	66642	-	-
obs	0.154	66642	98.1 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.848→41.296 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3584	0	15	472	4071

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3850
X-RAY DIFFRACTION	f_angle_d	1.27	5284
X-RAY DIFFRACTION	f_dihedral_angle_d	13.666	1368
X-RAY DIFFRACTION	f_chiral_restr	0.063	542
X-RAY DIFFRACTION	f_plane_restr	0.007	728

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.8483-1.8748	0.2178	120	0.1916	2175	2295	82
1.8748-1.9027	0.189	113	0.1888	2376	2489	88
1.9027-1.9325	0.1938	145	0.173	2411	2556	93
1.9325-1.9641	0.2011	128	0.166	2543	2671	95
1.9641-1.998	0.1661	143	0.1523	2636	2779	99
1.998-2.0343	0.1997	143	0.1541	2625	2768	99
2.0343-2.0735	0.1892	125	0.1564	2661	2786	100
2.0735-2.1158	0.1801	146	0.1505	2656	2802	100
2.1158-2.1618	0.1788	134	0.1455	2666	2800	100
2.1618-2.2121	0.1782	143	0.1499	2679	2822	100
2.2121-2.2674	0.1829	141	0.1521	2641	2782	100
2.2674-2.3287	0.1836	154	0.153	2651	2805	100
2.3287-2.3972	0.1854	150	0.1546	2658	2808	100
2.3972-2.4746	0.171	146	0.1593	2691	2837	100
2.4746-2.563	0.1919	153	0.1667	2653	2806	100
2.563-2.6656	0.1958	154	0.1666	2665	2819	100
2.6656-2.7869	0.2036	117	0.1725	2710	2827	100
2.7869-2.9338	0.1956	139	0.1714	2697	2836	100
2.9338-3.1176	0.2089	148	0.1684	2706	2854	100
3.1176-3.3582	0.1674	156	0.1549	2676	2832	100
3.3582-3.6959	0.1352	157	0.1355	2708	2865	100
3.6959-4.2303	0.1365	155	0.1203	2722	2877	100
4.2303-5.3279	0.1489	140	0.1234	2787	2927	100
5.3279-41.3068	0.1857	121	0.175	2878	2999	98

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	1.4587	-0.9838	-0.4107	2.8873	0.6047	2.2613	-0.1345	-0.2343	-0.2734	0.5298	0.0553	0.8296	0.1841	-0.5847	0.3471	0.2695	0.0888	0.2906	0.2534	0.0602	0.3693	55.4391	11.2688	41.0074
2	1.4413	0.6636	-0.5006	0.8515	1.0245	3.1361	-0.0024	0.0953	-0.0549	0.1615	-0.0406	0.7277	-0.1169	-0.5732	0.1291	0.1555	0.0444	0.0801	0.2065	0.0341	0.352	56.5205	12.4842	32.5068
3	0.9947	0.8546	-0.1076	1.9453	-1.1351	0.9173	-0.0818	-0.4066	-0.081	0.9596	-0.0344	0.3087	0.2076	0.0669	0.0871	0.4609	0.0854	0.1071	0.226	0.0387	0.199	67.6101	3.8858	42.5019
4	5.5308	-0.0454	-0.498	3.7602	2.5013	3.6679	-0.0025	-0.3205	0.3174	0.3542	0.0604	0.1069	-0.2998	0.0244	-0.0403	0.1894	0.0513	0.0941	0.1578	0.0329	0.1516	63.0695	19.2332	35.4559
5	1.6793	-0.0417	-0.7736	0.9709	0.3547	2.482	-0.1724	0.009	-0.4253	0.2937	0.0067	0.7822	0.3766	-0.4202	0.0803	0.1817	-0.0364	0.074	0.2195	0.0011	0.4448	56.4623	2.9146	30.1537
6	2.8176	-0.1355	-0.9892	2.7496	0.1283	2.9297	-0.0675	0.1791	-0.3438	-0.2141	-0.0323	0.5199	0.2809	-0.2728	0.0575	0.1427	0.0144	-0.0364	0.1234	-0.024	0.2097	63.6959	4.062	21.0049
7	1.5068	-0.0081	-0.0787	1.9467	-0.2436	1.4827	0.1639	0.338	-0.1065	-0.6441	-0.1389	0.1591	0.0432	-0.2011	-0.027	0.2533	0.0636	-0.0703	0.1866	-0.0173	0.1272	69.487	8.8981	12.8431
8	2.7118	0.4292	-0.2076	2.7592	0.0292	1.9902	0.098	-0.0131	-0.0267	-0.0563	-0.0747	0.238	-0.0782	-0.168	-0.0228	0.1272	0.0446	-0.0046	0.0956	0.0124	0.0962	68.3469	17.3627	23.8211
9	2.6845	0.8869	0.2784	4.3211	-1.2056	2.2037	-0.0877	0.5664	0.1143	-0.4319	-0.0428	-0.9461	-0.1417	0.7687	0.1471	0.1378	-0.0901	0.0209	0.4461	0.0568	0.259	96.1756	37.0181	6.2286
10	2.4153	-0.4021	-0.1115	1.3049	-1.532	4.4787	-0.0143	0.5441	-0.0097	-0.1538	0.0529	-0.3695	0.219	0.3988	-0.0267	0.1122	-0.0326	-0.0026	0.2876	0.0089	0.1433	87.4443	34.2198	5.1772
11	0.9466	1.2042	0.952	4.3773	0.4443	2.5292	-0.0644	0.0425	0.0158	0.24	-0.1536	-0.7419	-0.133	0.6244	-0.1861	0.1903	-0.0908	-0.128	0.341	0.0347	0.3325	96.9323	41.52	17.6239
12	6.1239	-1.3412	-0.1844	5.1592	0.0533	5.3894	-0.108	0.0287	-0.5993	0.2394	0.0215	-0.4968	0.5326	0.5667	-0.0225	0.0896	0.0039	-0.0056	0.2076	0.0205	0.2079	89.7332	27.0747	12.257
13	1.7655	0.3163	-0.0831	1.3133	-0.2037	1.9431	-0.189	0.4429	0.5723	-0.0558	0.0627	-0.0729	-0.4394	0.1773	0.0528	0.1946	-0.0558	-0.0602	0.2145	0.0956	0.1714	81.0059	43.065	8.1547
14	2.1317	0.1467	-0.2322	2.2718	-0.1617	1.7782	-0.1036	0.1122	0.3119	0.1565	0.0164	0.3066	-0.3309	-0.2097	0.0779	0.1453	0.0478	-0.021	0.1364	0.0072	0.1435	66.9382	38.4007	16.4082
15	2.1696	0.2798	-0.1559	2.2958	-0.0748	2.2171	-0.1055	0.0988	-0.051	0.1427	-0.0305	-0.0579	-0.0278	0.0918	0.1271	0.0953	0.0136	-0.0054	0.1102	0.0129	0.0826	77.5193	29.1507	16.0397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 57 through 85 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 106 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 120 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 121 through 138 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 139 through 173 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 174 through 209 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 210 through 263 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 264 through 292 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 60 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 106 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 120 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 121 through 138 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 139 through 209 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 263 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 264 through 292 )

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