PDB-7r1k: Phosphorylated Bacillus pumilus Lipase A

ID or keywords:

Entry

Database: PDB / ID: 7r1k

Title

Phosphorylated Bacillus pumilus Lipase A

Components

Lipase

Keywords

HYDROLASE / lipase / esterase / intermediate / complex

Function / homology

Lipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / Alpha/Beta hydrolase fold / hydrolase activity / DIETHYL PHOSPHONATE / OXALOACETATE ION / Lipase

Function and homology information

Biological species

Bacillus pumilus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Lund, B.A.

Funding support

Norway, 2items

Citation

Journal: Biochemistry / Year: 2022
Title: Structure and Mechanism of a Cold-Adapted Bacterial Lipase
Authors: Lund, B.A. / Svalberg, L. / Purg, M. / Chukwu, G. / Widersten, M. / Isaksen, G.V. / Brandsdal, B.O. / Aqvist, J.

History

Deposition	Feb 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 25, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7r1k.cif.gz	140.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7r1k.ent.gz	91.4 KB	Display	PDB format
PDBx/mmJSON format	7r1k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7r1k_validation.pdf.gz	673 KB	Display	wwPDB validaton report
Full document	7r1k_full_validation.pdf.gz	673.8 KB	Display
Data in XML	7r1k_validation.xml.gz	10.2 KB	Display
Data in CIF	7r1k_validation.cif.gz	13.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r1/7r1k ftp://data.pdbj.org/pub/pdb/validation_reports/r1/7r1k	HTTPS FTP

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Related structure data

Related structure data	7r25C 1ispS S: Starting model for refinement C: citing same article (ref.)
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
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Lipase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: homology

Unit cell

Length a, b, c (Å)	57.396, 42.843, 62.660
Angle α, β, γ (deg.)	90.000, 91.280, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

Components on special symmetry positions

ID	Model	Components
1	1	A-303- HOH

#1: Protein	Lipase Mass: 20483.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: L5 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) / References: UniProt: W8FKE7
#2: Chemical	ChemComp-OAA / OXALOACETATE ION Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₃O₅
#3: Chemical	ChemComp-DEP / DIETHYL PHOSPHONATE Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₁O₃P / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.88 Å³/Da / Density % sol: 34.58 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5 18-22 % PEG 4000 0.1-0.5 M lithium citrate 1:100 diluted paraoxon-ethyl mixed with enzyme Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
Detector	Type: Bruker PHOTON II / Detector: PIXEL / Date: Nov 9, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.5→20.93 Å / Num. obs: 47178 / % possible obs: 98.68 % / Redundancy: 6.3 % / B_iso Wilson estimate: 12.89 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.05036 / Net I/σ(I): 9.42
Reflection shell	Resolution: 1.5→1.554 Å / Redundancy: 3.9 % / R_merge(I) obs: 1.492 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4727 / CC_1/2: 0.399 / R_pim(I) all: 0.8465 / % possible all: 98.51

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Processing

Software

Name	Version	Classification
PHENIX	1.20rc4_4425	refinement
APEX 2		data collection
Aimless	0.7.3	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1isp

1isp

Resolution: 1.5→20.93 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.4494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1652	2291	4.86 %
R_work	0.1408	44856	-
obs	0.1419	47147	98.72 %

Solvent computation

Shrinkage radii: 0.4 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 17.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→20.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1358	0	17	99	1474

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0082	1440
X-RAY DIFFRACTION	f_angle_d	0.8729	1949
X-RAY DIFFRACTION	f_chiral_restr	0.0595	217
X-RAY DIFFRACTION	f_plane_restr	0.0097	258
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4366	522

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 (%)
1.5-1.53	0.3154	137	0.3105	2746	X-RAY DIFFRACTION	98.26
1.53-1.57	0.2993	180	0.2739	2797	X-RAY DIFFRACTION	99.23
1.57-1.61	0.2417	130	0.2493	2809	X-RAY DIFFRACTION	98.96
1.61-1.65	0.2659	173	0.234	2844	X-RAY DIFFRACTION	99.34
1.65-1.7	0.2514	150	0.2111	2783	X-RAY DIFFRACTION	99.32
1.7-1.75	0.2395	141	0.1928	2814	X-RAY DIFFRACTION	99.56
1.75-1.82	0.1979	148	0.1748	2831	X-RAY DIFFRACTION	99.67
1.82-1.89	0.172	124	0.1406	2894	X-RAY DIFFRACTION	99.93
1.89-1.98	0.1722	154	0.1231	2803	X-RAY DIFFRACTION	99.93
1.98-2.08	0.1564	159	0.1148	2814	X-RAY DIFFRACTION	99.33
2.08-2.21	0.1594	149	0.1142	2848	X-RAY DIFFRACTION	99.8
2.21-2.38	0.1173	146	0.1007	2829	X-RAY DIFFRACTION	99.07
2.38-2.62	0.1703	108	0.117	2738	X-RAY DIFFRACTION	95.79
2.62-3	0.1104	130	0.116	2839	X-RAY DIFFRACTION	99.16
3-3.77	0.1261	161	0.1132	2776	X-RAY DIFFRACTION	99.16
3.77-20.93	0.1362	101	0.1276	2691	X-RAY DIFFRACTION	93.07

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	3.70271174361	-3.97460086986	0.745916542626	8.49654899536	-3.2736757637	3.18238090676	0.0890967279646	0.0466816862177	-0.223274319923	-0.0113255903381	0.0359047710574	0.421154074068	-0.0219338461914	0.0543478567638	-0.0796949288856	0.0982120160252	-0.00431301836215	-0.0150172549864	0.112600045622	-0.00817586888406	0.0934253059367	-12.8770000883	-14.1505653849	9.73068771383
2	5.58535405352	-0.929341080706	1.33050135027	4.56082238727	-0.204312300169	3.60349365631	-0.0611176793493	0.128691984319	-0.256060906016	-0.0810006182966	0.0776036489789	0.227925314578	0.0181529761034	-0.113926847411	-0.0294293018365	0.0959595454958	-0.0175116443308	-0.0089515466428	0.111125046186	-0.0133861515713	0.0747996112833	-20.8634039317	-18.7046946987	6.41453236028
3	2.17635502379	-1.32328399929	-0.473949512378	1.21709214621	0.123326420766	0.170261888092	0.114672716867	0.589108086482	0.0695507297092	-0.156033418518	-0.053053392982	0.135369275218	0.16585903632	-0.0355625252692	-0.0645799289888	0.189895969234	0.00803889639297	-0.0161781119947	0.22542597402	0.0126247542412	0.116155164725	-18.9090597515	-11.2055452571	1.13322096688
4	4.71720591805	-2.30592209169	5.05971681021	2.84167994027	-2.62765075312	5.44086352951	-0.0025467119918	0.0769512106284	-0.0662928107959	0.100008659204	-0.0367953648532	-0.00367414593894	0.00786134671019	0.152789216801	0.0607513187522	0.122619414042	0.025441703397	0.0149767756596	0.143263193493	-0.00187284200716	0.132360026334	-2.76377475147	-20.358877648	12.0806302822
5	3.99918369451	-2.95093499194	3.50642611512	4.28668585721	-3.36949288193	6.95614918435	0.0188312254572	0.188757809034	0.0436854311298	-0.127758999072	-0.0882939289074	-0.19631103395	0.0763540774175	0.197114543864	0.0179558769415	0.0950422712731	0.000111578102295	0.00979470211389	0.118214405044	-0.00108963112681	0.116609859171	-3.15813922085	-9.79075338415	6.59310026503
6	1.93193609061	0.280863149372	0.0418413166906	2.37265691206	-0.833455522937	2.86752456346	-0.0123421623788	-0.0749144449212	0.0325792642596	0.031878906852	0.0453502801185	-0.142695202248	-0.107817347396	0.132683057699	-0.00924726451223	0.0961589466392	0.00708482605971	0.010373683692	0.0995347843435	-0.0129618985309	0.0845529397568	-8.48840192624	-8.23638251036	14.5714139794
7	2.22909431122	0.628838483821	-0.717294579207	1.01326271959	-0.344270951085	1.00571912082	0.0243023165212	-0.0851983624433	0.118789117251	0.0490479609607	0.0116994127012	-0.0738839328611	-0.0692356347684	0.0456480893726	-0.0549626262138	0.115833290373	-0.000781426626793	0.000280138590782	0.099516351815	-0.0194056532946	0.0930836805559	-10.3048791652	-6.86595969841	16.4780605453
8	4.17421690832	-0.394981454078	-0.648909007157	4.99714348705	-0.317275039768	2.69484659459	-0.0419613834579	-0.0984258293005	0.507317738187	0.0907160726024	0.077202216934	0.138750337778	-0.387819985522	0.0818730937712	-0.107293740128	0.148020365381	-0.0189393728298	-0.00284114888388	0.137912989036	-0.0353289895157	0.185029699368	-10.2040876221	1.24729913574	20.0830069869
9	1.06842777299	-0.183168790867	0.0673772345599	2.74014980393	-0.251490206587	1.46854197915	0.032012332312	-0.135564391583	-0.0859406252977	0.152022438173	-0.0299519338367	0.0962126030647	0.107221757382	-0.0571560575806	0.024778535423	0.135270059366	-0.00558275068477	0.0176138455669	0.134442568879	0.00166736228078	0.0955861042775	-18.6224299268	-14.8975439958	25.5994237823
10	2.24988572183	1.12263326628	0.208227255914	7.21016584956	0.355731640638	1.15227502448	0.0648191648929	-0.106604286246	0.0640876858931	0.17764890162	-0.106332226598	0.210907673883	0.0509503718332	-0.0707021241181	0.0121574753575	0.0963813580471	-0.00660677413802	-0.00196881905704	0.135521221074	-0.00436282815432	0.0956389619343	-25.0516137043	-14.7831521336	15.452663166
11	3.78621566306	2.18396095868	5.10096472855	3.69148620549	3.27475147623	8.21644435584	-0.104400056537	0.0208347883394	0.223965620948	-0.00325039703977	0.109412525355	0.0289325640611	-0.488871076053	0.128598508611	-0.11576776383	0.174746260717	0.000807336723126	0.0106445971298	0.135231025613	-0.0371188044283	0.158055273858	-17.8324380429	1.73232502569	21.6992671661

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 4 through 16 )	4 - 16	1 - 13
2	2	chain 'A' and (resid 17 through 30 )	17 - 30	14 - 27
3	3	chain 'A' and (resid 31 through 39 )	31 - 39	28 - 36
4	4	chain 'A' and (resid 40 through 48 )	40 - 48	37 - 45
5	5	chain 'A' and (resid 49 through 67 )	49 - 67	46 - 64
6	6	chain 'A' and (resid 68 through 90 )	68 - 90	65 - 87
7	7	chain 'A' and (resid 91 through 109 )	91 - 109	88 - 106
8	8	chain 'A' and (resid 110 through 124 )	110 - 124	107 - 121
9	9	chain 'A' and (resid 125 through 158 )	125 - 158	122 - 155
10	10	chain 'A' and (resid 159 through 174 )	159 - 174	156 - 171
11	11	chain 'A' and (resid 175 through 184 )	175 - 184	172 - 181

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