PDB-8cr7: Crystal structure of recombinant LasB from Pseudomonas aeruginosa PA7

ID or keywords:

Entry

Database: PDB / ID: 8cr7

Title

Crystal structure of recombinant LasB from Pseudomonas aeruginosa PA7

Components

Pro-elastase

Keywords

HYDROLASE / LasB /

Pseudomonas aeruginosa / recombinant

Function / homology

Function and homology information

pseudolysin / protein transport by the Sec complex /

protein secretion by the type II secretion system / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation /

metalloendopeptidase activity /

endopeptidase activity /

proteolysis / extracellular region /

metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa PA7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Kolling, D. / Koehnke, J.

Funding support

Germany, 1items

Citation

Journal: Chembiochem / Year: 2023
Title: Facile Production of the Pseudomonas aeruginosa Virulence Factor LasB in Escherichia coli for Structure-Based Drug Design.
Authors: Kolling, D. / Haupenthal, J. / Hirsch, A.K.H. / Koehnke, J.

History

Deposition	Mar 7, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2023	Group: Database references / Category: citation / citation_author Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cr7.cif.gz	429.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8cr7.ent.gz	287.5 KB	Display	PDB format
PDBx/mmJSON format	8cr7.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/cr/8cr7 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8cr7	HTTPS FTP

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Related structure data

Related structure data	8cr3C 8cr4C 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

Deposited unit

A: Pro-elastase

B: Pro-elastase

hetero molecules

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

1

A: Pro-elastase

hetero molecules

defined by author
Evidence: gel filtration
55.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pro-elastase

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.156, 64.274, 73.401
Angle α, β, γ (deg.)	90.000, 108.095, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Pro-elastase Mass: 55577.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA7 (bacteria) / Gene: lasB, PA3724 / Production host: Escherichia coli (E. coli) / Variant (production host): Lemo21 / References: UniProt: P14756
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30% (v/v) MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 1.5→43.11 Å / Num. obs: 242845 / % possible obs: 99.4 % / Redundancy: 2.8 % / B_iso Wilson estimate: 17.01 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.044 / R_rim(I) all: 0.076 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.5→1.53 Å / R_merge(I) obs: 0.365 / Num. unique obs: 4239 / CC_1/2: 0.868 / R_pim(I) all: 0.258 / R_rim(I) all: 0.449

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
pointless		data scaling
PHASER		phasing
autoPROC		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→43.11 Å / SU ML: 0.1397 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1893	4270	4.97 %
R_work	0.1638	81645	-
obs	0.1651	85914	99.28 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→43.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4622	0	4	646	5272

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0125	4748
X-RAY DIFFRACTION	f_angle_d	1.184	6434
X-RAY DIFFRACTION	f_chiral_restr	0.0707	644
X-RAY DIFFRACTION	f_plane_restr	0.0103	858
X-RAY DIFFRACTION	f_dihedral_angle_d	5.4443	664

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 (%)
1.5-1.52	0.2357	149	0.217	2621	X-RAY DIFFRACTION	99.28
1.52-1.53	0.2468	145	0.2154	2767	X-RAY DIFFRACTION	99.66
1.53-1.55	0.2693	131	0.2109	2704	X-RAY DIFFRACTION	99.58
1.55-1.57	0.2217	160	0.1996	2728	X-RAY DIFFRACTION	99.76
1.57-1.59	0.2293	159	0.1962	2689	X-RAY DIFFRACTION	99.65
1.59-1.62	0.2157	136	0.1875	2700	X-RAY DIFFRACTION	99.44
1.62-1.64	0.223	151	0.1871	2710	X-RAY DIFFRACTION	99.51
1.64-1.66	0.2153	156	0.1891	2713	X-RAY DIFFRACTION	99.38
1.66-1.69	0.2348	138	0.1812	2725	X-RAY DIFFRACTION	99.62
1.69-1.72	0.2138	137	0.1771	2724	X-RAY DIFFRACTION	99.65
1.72-1.75	0.1821	130	0.1719	2761	X-RAY DIFFRACTION	99.55
1.75-1.78	0.194	147	0.1677	2688	X-RAY DIFFRACTION	99.51
1.78-1.81	0.1869	156	0.1685	2710	X-RAY DIFFRACTION	99.48
1.81-1.85	0.2245	135	0.1603	2755	X-RAY DIFFRACTION	99.52
1.85-1.89	0.1865	121	0.1608	2743	X-RAY DIFFRACTION	99.51
1.89-1.93	0.1727	136	0.1598	2687	X-RAY DIFFRACTION	99.65
1.93-1.98	0.1665	149	0.1545	2759	X-RAY DIFFRACTION	99.76
1.98-2.04	0.1966	145	0.1571	2708	X-RAY DIFFRACTION	99.62
2.04-2.1	0.1718	120	0.1497	2740	X-RAY DIFFRACTION	99.24
2.1-2.16	0.1626	163	0.149	2709	X-RAY DIFFRACTION	99.41
2.16-2.24	0.1705	132	0.148	2693	X-RAY DIFFRACTION	98.88
2.24-2.33	0.1961	154	0.1528	2728	X-RAY DIFFRACTION	99.35
2.33-2.44	0.1691	145	0.1517	2730	X-RAY DIFFRACTION	99.21
2.44-2.56	0.183	120	0.1541	2752	X-RAY DIFFRACTION	99.51
2.56-2.73	0.1934	140	0.1585	2724	X-RAY DIFFRACTION	99.48
2.73-2.94	0.1861	144	0.1585	2751	X-RAY DIFFRACTION	98.94
2.94-3.23	0.1773	142	0.1653	2724	X-RAY DIFFRACTION	98.96
3.23-3.7	0.1875	148	0.1545	2707	X-RAY DIFFRACTION	98.31
3.7-4.66	0.1638	145	0.1432	2732	X-RAY DIFFRACTION	97.72
4.66-43.11	0.2163	136	0.2013	2763	X-RAY DIFFRACTION	97.28

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	2.01357564916	-0.161968915017	-1.75955456727	1.2907544391	0.445623458179	3.41703103357	-0.152634205609	0.0151652239493	-0.33062926611	0.0223046611354	-0.0804842054214	0.0556116852488	0.250103420678	-0.142116216356	0.124059013545	0.18224643807	-0.0039386626389	0.01597485539	0.106608321993	-0.00390630208931	0.205974181043	-17.6758395723	-1.99854270267	7.78668303038
2	0.678311790018	0.40536388398	-0.0221366500449	1.10296885018	-0.757306650425	1.75822962079	0.0387167955492	-0.148990872634	-0.0281494631288	0.226765932929	-0.050186671276	0.123628384663	-0.0922863121561	-0.157426707653	-0.00841196448109	0.16258035676	0.0122624441056	0.00141080496297	0.160099107025	-0.0249044225114	0.179826600966	-21.471521589	10.7195326088	13.8493365958
3	1.80759692742	0.108293770728	-0.0796079382672	0.168689877758	-0.154090767749	0.991059894407	0.0305489988863	-0.0487538926546	-0.047798773387	0.0103746031549	-0.0900786413653	-0.00162795975776	0.0830992160423	-0.0641887493536	0.0222851386577	0.14803463313	-0.00830076867293	-0.00411227838888	0.106085250282	0.0012310666476	0.164208219014	-12.5178961671	5.70929228504	11.3365937545
4	1.29951825523	-0.114526012419	0.136402159484	0.688325396418	0.276141241559	1.5518024092	0.0120345625906	0.00192245786302	0.0515972537028	-0.0707097038273	0.0167850661626	0.0899523529265	-0.294553450712	0.0677671593405	0.0520056186067	0.182606284212	-0.0125385398024	-0.000578049762093	0.115736452626	0.00568049486816	0.176681921893	-11.9135532455	15.9335704072	8.37025097882
5	1.56311959387	0.433037022913	0.55208627617	0.365303717779	0.102079778046	0.313635848708	0.00259107232488	-0.0152127533598	0.123822840346	-0.0597102000791	-0.0293929009916	0.00749569217776	-0.112620966284	-0.0189304235787	0.0131858846956	0.177702973404	-0.00971759066007	-0.0018750574089	0.116559648115	0.00888462703772	0.164970534027	-5.19988752754	14.6960003052	4.96269659225
6	1.57488156323	0.540265772239	-0.84266518312	2.64656819838	-1.20358448648	2.78889325424	-0.014863438497	-0.0814327950737	-0.0527940375414	-0.0999521867474	0.030384363527	0.0652754615712	0.114572545468	-0.121742502338	0.0275092146108	0.139450012385	-0.00416314372106	-0.00138608936651	0.128836339972	0.00969201790283	0.147344783441	2.76099871764	8.05505287747	8.13839763687
7	3.28148957777	-0.656489682772	0.902326608508	1.10522042836	-0.157854384494	0.267736711571	0.120608338265	0.211881158436	-0.343742384841	0.0430545962913	-0.0775243407791	0.129404645208	0.0922765975577	-0.00646033517959	-0.0622233523633	0.191725938818	-0.000392385111481	-0.011783154342	0.146740826562	-0.00966371416485	0.193856394275	-0.355346307733	0.953048293677	-0.875566114581
8	1.54721334227	0.0191344699081	-0.681418912149	0.530282105231	0.208313179582	2.05520664041	0.0224470590184	-0.0240863933216	-0.0375882243134	-0.0293630441688	-0.0222676635553	-0.0448245463651	0.00841234476206	0.0438471771916	-0.000328045411494	0.131512809649	-0.00721144509511	-0.00835578701823	0.103805434368	0.015663519555	0.163627408793	10.2332075957	8.13960716282	4.14734283434
9	1.36519320367	-0.25107017723	-0.859573081638	1.33875403804	-0.330631371036	1.70237369045	0.0805806058867	-0.235608354133	0.114899271071	0.0113173588501	-0.0501652221779	-0.0348051253363	-0.264898627464	0.272386339435	-0.0199438439103	0.160562578921	-0.0501442984136	0.00338241406275	0.176483174503	-0.000375406190848	0.182952228634	16.3875128989	15.4035737644	12.639776333
10	1.49015124489	-0.266382980176	-0.988598229596	0.468434470595	-0.312398347947	3.37312445399	-0.0712862258553	-0.165365791089	-0.0677180344381	0.0258316106841	-0.0616529998158	-0.131374420676	0.126448033964	0.295271988555	0.0597204457375	0.142629316956	-0.0129985239814	-0.0146888891421	0.212869633055	0.0278255987552	0.190623473017	19.6735454573	6.10694365702	10.6538356844
11	1.26905837329	0.140862959594	-0.616932601658	2.2221902917	0.130799833675	4.0113346201	0.0205150509861	0.304848115057	-0.179835433629	0.0678590068046	0.0405530755621	0.033968460742	0.468060246152	0.697998009233	-0.128737007811	0.222245601519	0.115670944587	-0.044988528527	0.303546901361	-0.0363610931895	0.131663180166	22.3910951111	-7.04382224528	47.3711097175
12	1.61442713079	0.432938166922	0.507825563904	1.18454933578	0.860654072855	2.63649466639	-0.102467057833	0.58021559576	0.121088037748	-0.126646147653	0.226049476925	-0.147694771273	-0.116807824844	0.660688787675	-0.080352534611	0.148260115414	-0.0261963792893	0.0104300704088	0.416555315063	0.0243245310763	0.13801224136	21.2935362087	3.15399223219	39.4418618447
13	2.70101683889	-0.124508620706	1.12273441455	1.33799174876	0.168175104517	3.23655473225	-0.122081909982	0.406696196577	0.251864856889	0.0311787673468	0.130396905469	0.114852418226	-0.281243890561	0.246464323145	-0.0626142261348	0.176854415808	-0.0122325912454	-0.0143734713476	0.215213403877	0.0359010917191	0.184599018196	15.5441534594	8.96518029586	48.4714350155
14	2.02927218644	0.0620611253912	-0.523730966681	1.08870784458	0.40642484005	2.19319870449	0.0552137829774	0.359024839295	0.326082811447	-0.044314507436	-0.028189856812	-0.062357043277	-0.103477677217	0.0291613138282	0.000348003760131	0.100798820907	0.00866820787145	0.0106987804248	0.149757789827	0.0645140126601	0.140716033461	3.18389168535	6.05994166549	41.7116206755
15	2.39845576134	0.75312117521	0.87008781076	0.264809501081	0.32481955694	1.37462084677	-0.0372310597626	-0.0649467375245	0.0227965747939	0.0463082737996	0.0267484759889	-0.0100078597962	0.0565423575362	0.0525349684085	-0.0624543815694	0.200515799206	0.00345315861185	0.00333654235526	0.161428532685	0.0137809592342	0.169452232248	6.81831929596	-1.55476464633	54.1949231167
16	1.86797195854	-0.062331012055	-0.90438140114	0.889513950415	0.33500463009	1.98859651555	0.0307721921511	0.36884690509	0.118331954454	0.00145740177728	0.0045618632565	0.0603787449986	0.00109962664918	-0.353248405032	-0.0201371437232	0.104515708134	0.00172810969927	-0.00889229524714	0.184037253539	0.0537567887841	0.106800919147	-8.44773713196	3.27603261949	44.214582333

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 1 through 17 )	A	A	1 - 17	1 - 17
2	2	chain 'A' and (resid 18 through 61 )	A	A	18 - 61	18 - 61
3	3	chain 'A' and (resid 62 through 91 )	A	A	62 - 91	62 - 91
4	4	chain 'A' and (resid 92 through 112 )	A	A	92 - 112	92 - 112
5	5	chain 'A' and (resid 113 through 156 )	A	A	113 - 156	113 - 156
6	6	chain 'A' and (resid 157 through 179 )	A	A	157 - 179	157 - 179
7	7	chain 'A' and (resid 180 through 202 )	A	A	180 - 202	180 - 202
8	8	chain 'A' and (resid 203 through 257 )	A	A	203 - 257	203 - 257
9	9	chain 'A' and (resid 258 through 278 )	A	A	258 - 278	258 - 278
10	10	chain 'A' and (resid 279 through 298 )	A	A	279 - 298	279 - 298
11	11	chain 'B' and (resid 1 through 17 )	B	D	1 - 17	1 - 17
12	12	chain 'B' and (resid 18 through 112 )	B	D	18 - 112	18 - 112
13	13	chain 'B' and (resid 113 through 134 )	B	D	113 - 134	113 - 134
14	14	chain 'B' and (resid 135 through 179 )	B	D	135 - 179	135 - 179
15	15	chain 'B' and (resid 180 through 199 )	B	D	180 - 199	180 - 199
16	16	chain 'B' and (resid 200 through 298 )	B	D	200 - 298	200 - 298

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