PDB-7wu1: Crystal structure of phospholipase D from Moritella sp. JT01

ID or keywords:

Entry

Database: PDB / ID: 7wu1

Title

Crystal structure of phospholipase D from Moritella sp. JT01

Components

Phospholipase D

Keywords

HYDROLASE / Glycerophosphate phosphodiesterase / Hydrolysis / glycerophosphorylcholine / lysophosphorylcholine

Function / homology

Function and homology information

phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipase D / phospholipase D activity
Similarity search - Function

Biological species

Moritella sp. JT01 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Wang, Y.H. / Mao, X.J. / Wang, J. / Wang, F.H.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Crystal structure of phospholipase D from Moritella sp. JT01
Authors: Wang, Y.H. / Mao, X.J. / Wang, J. / Wang, F.H.

History

Deposition	Feb 5, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wu1.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb7wu1.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	7wu1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wu1_validation.pdf.gz	511.9 KB	Display	wwPDB validaton report
Full document	7wu1_full_validation.pdf.gz	563.2 KB	Display
Data in XML	7wu1_validation.xml.gz	121 KB	Display
Data in CIF	7wu1_validation.cif.gz	169.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/7wu1 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wu1	HTTPS FTP

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Related structure data

Related structure data	1f0iS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phospholipase D

B: Phospholipase D

C: Phospholipase D

D: Phospholipase D

E: Phospholipase D

F: Phospholipase D

hetero molecules

373 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	93.897, 216.644, 277.708
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Phospholipase D Mass: 61993.965 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moritella sp. JT01 (bacteria) / Gene: AKG98_3441 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A137SLD1, phospholipase D
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	... ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 67.62 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium/HCl pH 7.4, 0.8 M Potassium sodium tartrate tetrahydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.3→23.36 Å / Num. obs: 484769 / % possible obs: 99.69 % / Redundancy: 9.7 % / B_iso Wilson estimate: 65.73 Å² / CC_1/2: 0.304 / Net I/σ(I): 0.6
Reflection shell	Resolution: 2.3→2.38 Å / Num. unique obs: 24724 / CC_1/2: 0.304

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F0I

1f0i

Resolution: 2.3→19.81 Å / SU ML: 0.431 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 28.9766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2157	3873	0.8 %
R_work	0.2116	480896	-
obs	0.2116	484769	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 78.77 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25452	0	55	984	26491

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0096	26003
X-RAY DIFFRACTION	f_angle_d	0.9358	35381
X-RAY DIFFRACTION	f_chiral_restr	0.053	4040
X-RAY DIFFRACTION	f_plane_restr	0.006	4552
X-RAY DIFFRACTION	f_dihedral_angle_d	14.8668	9239

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 (%)
2.3-2.33	0.3808	133	0.4146	16958	X-RAY DIFFRACTION	98.73
2.33-2.36	0.4345	141	0.3995	17217	X-RAY DIFFRACTION	99.93
2.36-2.39	0.3788	138	0.3909	17118	X-RAY DIFFRACTION	99.92
2.39-2.42	0.43	139	0.3757	17183	X-RAY DIFFRACTION	99.92
2.42-2.46	0.3855	140	0.3716	17220	X-RAY DIFFRACTION	99.91
2.46-2.49	0.3988	137	0.3684	17140	X-RAY DIFFRACTION	99.95
2.49-2.53	0.3483	140	0.3465	17228	X-RAY DIFFRACTION	99.9
2.53-2.57	0.3193	139	0.3336	17241	X-RAY DIFFRACTION	99.95
2.57-2.62	0.3913	139	0.3221	17162	X-RAY DIFFRACTION	99.95
2.62-2.66	0.292	138	0.3187	17147	X-RAY DIFFRACTION	99.96
2.66-2.72	0.294	136	0.3012	17184	X-RAY DIFFRACTION	99.9
2.72-2.77	0.2978	138	0.2926	17214	X-RAY DIFFRACTION	99.61
2.77-2.83	0.2706	140	0.2844	17108	X-RAY DIFFRACTION	99.57
2.83-2.9	0.3045	140	0.2679	17139	X-RAY DIFFRACTION	99.97
2.9-2.97	0.2831	141	0.2631	17151	X-RAY DIFFRACTION	99.97
2.97-3.05	0.2734	142	0.2422	17321	X-RAY DIFFRACTION	99.97
3.05-3.14	0.2684	132	0.2385	17177	X-RAY DIFFRACTION	99.99
3.14-3.24	0.2283	139	0.2356	17205	X-RAY DIFFRACTION	99.99
3.24-3.35	0.2154	137	0.2225	17217	X-RAY DIFFRACTION	99.97
3.35-3.49	0.2195	135	0.2177	17176	X-RAY DIFFRACTION	100
3.49-3.65	0.1974	137	0.2046	17084	X-RAY DIFFRACTION	99.66
3.65-3.84	0.2065	139	0.1922	17141	X-RAY DIFFRACTION	99.89
3.84-4.07	0.2057	139	0.1831	17312	X-RAY DIFFRACTION	100
4.07-4.39	0.1529	138	0.1657	17115	X-RAY DIFFRACTION	100
4.39-4.82	0.165	138	0.1595	17208	X-RAY DIFFRACTION	100
4.82-5.51	0.1644	141	0.1677	17207	X-RAY DIFFRACTION	99.88
5.51-6.89	0.1595	137	0.1862	17168	X-RAY DIFFRACTION	100
6.89-19.81	0.1815	140	0.1642	17155	X-RAY DIFFRACTION	99.65

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	2.59480744222	0.536870368417	-0.513664461465	2.4031787354	-0.0249933370219	1.38544586097	-0.052297375984	0.138346925324	0.385277662939	-0.334720315484	0.0516576628771	0.103608393483	0.0414261253332	0.0162996078385	0.00422927278875	0.472082018049	0.0112563548015	-0.0713226453643	0.591449121849	-0.000525498648473	0.423817389903	71.9575042321	150.855675448	128.044632886
2	1.57218961607	0.767359650994	-1.37376667281	2.8268076476	0.693949532601	3.57459832814	-0.0710370606773	-0.262481157649	0.127216419843	0.23400792421	0.0515494538121	0.0782469289184	0.105548661109	0.134094936696	0.0962728520679	0.321542154759	0.0134974157176	-0.0624820343827	0.625251496698	-0.0163817591591	0.569176756481	68.8975739876	157.500751645	143.649712035
3	1.27141176769	-0.242278115364	-0.00422598826242	2.02917339615	0.141626960881	1.17534266616	-0.0739727054647	0.0538702832271	-0.161092129327	-0.19752716291	-0.00530262580674	0.404844344766	0.240857478322	-0.192926017784	0.0645052429616	0.448075298188	-0.0583127325352	-0.0491948593854	0.587737570296	-0.00690490600407	0.569360867237	63.0890488397	137.740261352	134.710670129
4	2.05345625141	0.720006835741	0.87088245319	3.0343239036	0.683192020654	2.09973780384	0.205872307729	-0.337690974973	-0.0832717019605	0.527622171398	-0.0389700152416	0.359102746121	0.25500733072	-0.32752915614	-0.131501669672	0.63300771846	-0.00747049817986	0.0934509392722	0.602616384304	0.0297254813422	0.699523334775	23.8199228833	165.935069824	203.600644716
5	2.46248480304	-0.986032755919	0.434041941048	4.23879889793	0.00469660783484	3.32489262427	0.270891782885	-0.164345105881	-0.390562684872	0.291164130501	-0.0913768776909	-0.302019643593	0.433113263784	0.0377307676112	-0.113161123988	0.739256530223	-0.0657187759284	-0.0411968607241	0.542606603879	0.0677710414851	0.662277265179	30.7212084972	149.824354498	204.517526598
6	2.31678573417	0.253664358966	-0.405836678269	2.50100155381	-0.135609938209	1.43888902587	0.047507495191	-0.0560008791427	-0.456527991364	-0.0942488592382	-0.0220639970718	0.0928420025758	0.245589379663	-0.0199931702755	-0.0490195033749	0.625802513639	-0.0194828127882	-0.00329627591154	0.495354512969	0.0205858268875	0.546662813161	31.6714589062	155.385714191	194.76974818
7	1.66275225072	0.0919212203959	0.725720490576	1.94135124505	0.0212821300561	1.77393805406	0.0149309375015	0.0115059786884	-0.361182153028	-0.114810247073	-0.019999335039	0.268639863993	0.383081301304	-0.121627421883	-0.0207260728176	0.802930498181	-0.0753963493602	-0.0299525187172	0.624198060666	0.0206484537675	0.872381062776	22.7497699446	146.566197233	193.076086462
8	2.52983444996	0.684743005956	0.652673060487	2.15150337001	0.114053439758	2.05724999212	-0.162793006152	0.339425106338	0.140545448759	-0.51097131472	0.118516380551	0.204010454168	-0.248602075933	0.00618889800594	0.02205784884	0.712179507825	-0.00195774023453	-0.0260762196891	0.541054178657	0.0161789984759	0.499732579427	31.9374358795	173.415233099	183.137905684
9	1.69406214145	-0.311548098327	-0.913479849344	1.88218919296	0.27208987995	2.50705219679	0.179040222274	-0.0355920682399	0.265788598137	-0.0229619379446	0.108159588285	-0.270339077309	-0.286170361016	0.27164813591	-0.236005666401	0.517106105515	-0.0773696070061	0.0463321516893	0.614709878015	-0.101040453268	0.567961997096	72.6471336526	184.085584067	181.516473933
10	1.58013203027	-0.96752644673	-1.50447042059	4.83153149026	-0.44375302746	5.06237590685	-0.0964264552528	0.126093995145	-0.0655094314152	0.0317734140144	0.266738791765	0.0901057440155	0.259686871881	-0.00902202694349	-0.155269466492	0.448942421494	0.00595477259402	-0.0474683052816	0.660432711227	-0.0609806212285	0.509501450372	73.0013064545	172.910567745	171.006861845
11	1.35154808872	-0.391672481569	-0.617009278868	1.2163356773	0.599051302177	2.28657733684	-0.0692998785941	-0.153341495247	-0.116563139559	0.315143458089	0.135120823298	-0.0773362496692	0.236434825093	0.3270146463	-0.0744619081303	0.552000240905	0.0406455079465	-0.049290149612	0.603711192766	-0.0239957888796	0.511966828276	68.7224990155	170.460433595	189.65286726
12	1.59329748457	0.461127961488	-0.245925810121	2.00827753084	-0.562031035552	1.6513490065	0.0638315136236	-0.113202180099	-0.608267181844	0.0569328311286	0.0379957803225	-0.1504655184	0.314069325461	-0.278890093784	-0.0886925434968	0.669885921546	0.0632294682814	-0.0913781843387	0.650120452316	0.108973785902	0.895952133083	81.6602851538	100.906498096	154.830790957
13	1.70985937048	0.615899498338	-0.150377310701	2.51596061655	-0.40113812803	1.21802391364	0.10466328489	-0.19421264732	-0.333602983548	0.300747291135	-0.0415630365793	-0.45309228279	0.0431385262686	0.108987088396	-0.0489197969843	0.515999955748	0.0614511172628	-0.0597587329147	0.552934063919	0.0585486105217	0.655624150484	90.2099357304	117.99782076	155.386524798
14	2.60681618494	0.319556572993	-0.69047546859	2.54816796433	-0.157981000508	1.06614228354	-0.0443102355106	-0.207333455593	0.416563460245	0.887736796391	-0.0214906351914	0.108357382182	-0.246003433602	-0.00328309355844	0.118892077235	1.13268459119	-0.0350973896617	-0.0937636016566	0.607249394459	0.04298820834	0.665439179979	45.3240066463	111.028509817	224.441068103
15	1.47301229112	-0.901512227912	-0.829571548537	2.07189004883	-0.534672573826	1.45982044304	-0.0869393214718	0.0237571836032	0.540476415046	0.339049337936	-0.0239414848646	-0.103565817438	-0.405796431979	-0.153959168992	-0.0044461374634	1.0713750377	-0.0409602110729	-0.12034418583	0.596442689602	0.033848618263	0.866300087525	43.7966003416	124.558252501	217.032932196
16	1.3368991733	-0.963629040728	-0.478131566955	2.53531640674	0.272663409834	0.991246150803	0.0931438188454	0.156198426379	0.431675702785	-0.0758946557958	-0.154252633709	-0.246735169099	-0.394877995207	-0.0476401597129	0.0287637340048	0.925725316026	-0.0546224345208	-0.0826767239738	0.651046231583	0.145708504077	0.897032445293	47.4065062126	124.861308523	204.420972318
17	1.50072998434	-0.296039425624	0.132476515437	1.92168081412	0.0285994977802	0.628849532712	-0.125802181825	-0.0746073367874	0.48918027332	0.362809508474	-0.00878581979973	-0.536006000461	-0.372534473184	0.0742579646092	0.0624132797561	1.05079200727	-0.0573881628692	-0.164216751121	0.591290384661	0.061081027232	0.871989016204	53.6409109465	122.668118649	217.207631953
18	1.65056839152	-0.436576706399	-0.0999033894928	2.32376976112	0.138493558054	0.805102132391	-0.145993675971	0.0203066471174	0.152078340703	0.192867172643	-0.014745314304	-0.390397654515	-0.00553745771644	0.107596902527	0.172110585452	0.771187730475	-0.0581656662424	-0.0508586081424	0.576603530945	0.146147875066	0.647949879124	56.9336274408	97.9784296784	209.422981315
19	1.57656940459	-0.655873911523	-0.213266881096	2.57588552171	-0.769736240416	1.97655778767	0.0938697933189	0.43774311372	-0.267649319502	-0.270050015599	-0.277983655759	0.266753356057	0.206751807474	-0.19768568149	0.200460529594	0.634744901423	-0.0807624518717	-0.118532256197	0.806840577437	-0.0688979280731	0.617144363254	36.3274148194	82.8464611355	176.723804086
20	2.57624083492	0.791538338259	-2.3855681956	5.15831314617	-0.603784040231	2.19330238066	0.254450093769	0.182197764452	-0.121230963564	-0.00392193420319	-0.535168432026	-0.0942961349915	-0.0373872299296	-0.0909070763581	0.111707786578	0.679583784257	0.0539868921979	-0.0984003980038	0.949972867332	0.0478556965736	0.593076396563	44.6669438894	89.0690362927	172.168414038
21	1.14613902195	-0.422632980741	-0.33202841477	1.75353055185	0.27637547111	1.70801884638	0.146260417843	0.405141679514	-0.0104334209845	-0.216325665451	-0.25188930935	0.241864532183	-0.270875745922	-0.285105491905	0.0979442744495	0.621475388827	0.0355910537056	-0.100666680535	0.808801090114	0.0628805589691	0.577544885714	35.0743837111	97.9341323811	179.442166308

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 11 through 112 )	A	A	11 - 112	1 - 102
2	2	chain 'A' and (resid 113 through 217 )	A	A	113 - 217	103 - 201
3	3	chain 'A' and (resid 218 through 554 )	A	A	218 - 554	202 - 538
4	4	chain 'B' and (resid 11 through 112 )	B	D	11 - 112	1 - 102
5	5	chain 'B' and (resid 113 through 217 )	B	D	113 - 217	103 - 205
6	6	chain 'B' and (resid 218 through 296 )	B	D	218 - 296	206 - 284
7	7	chain 'B' and (resid 297 through 363 )	B	D	297 - 363	285 - 351
8	8	chain 'B' and (resid 364 through 554 )	B	D	364 - 554	352 - 542
9	9	chain 'C' and (resid 10 through 112 )	C	E	10 - 112	1 - 103
10	10	chain 'C' and (resid 113 through 195 )	C	E	113 - 195	104 - 186
11	11	chain 'C' and (resid 196 through 554 )	C	E	196 - 554	187 - 542
12	12	chain 'D' and (resid 10 through 235 )	D	F	10 - 235	1 - 223
13	13	chain 'D' and (resid 236 through 554 )	D	F	236 - 554	224 - 542
14	14	chain 'E' and (resid 10 through 112 )	E	G	10 - 112	1 - 103
15	15	chain 'E' and (resid 113 through 195 )	E	G	113 - 195	104 - 186
16	16	chain 'E' and (resid 196 through 260 )	E	G	196 - 260	187 - 251
17	17	chain 'E' and (resid 261 through 363 )	E	G	261 - 363	252 - 354
18	18	chain 'E' and (resid 364 through 554 )	E	G	364 - 554	355 - 545
19	19	chain 'F' and (resid 10 through 112 )	F	H	10 - 112	1 - 103
20	20	chain 'F' and (resid 113 through 151 )	F	H	113 - 151	104 - 142
21	21	chain 'F' and (resid 152 through 554 )	F	H	152 - 554	143 - 545

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