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- PDB-8cr3: Crystal structure of recombinant LasB from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 8cr3
TitleCrystal structure of recombinant LasB from Pseudomonas aeruginosa PAO1
ComponentsPro-elastase
KeywordsHYDROLASE / 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
PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsKolling, D. / Koehnke, J.
Funding support1items
OrganizationGrant numberCountry
Other government16GW0346
CitationJournal: 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
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pro-elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7783
Polymers55,6731
Non-polymers1052
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-51 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.542, 89.875, 41.340
Angle α, β, γ (deg.)90.000, 113.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Pro-elastase


Mass: 55672.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.116→44.938 Å / Num. obs: 190922 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.53 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.048 / Rrim(I) all: 0.086 / Net I/σ(I): 8.9
Reflection shellResolution: 1.116→1.136 Å / Rmerge(I) obs: 0.565 / Num. unique obs: 5145 / CC1/2: 0.736 / Rpim(I) all: 0.38 / Rrim(I) all: 0.683

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→28.59 Å / SU ML: 0.0968 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 18.4889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1701 9501 4.98 %
Rwork0.1618 181421 -
obs0.1622 190922 92.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.92 Å2
Refinement stepCycle: LAST / Resolution: 1.12→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 2 410 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692379
X-RAY DIFFRACTIONf_angle_d1.05053224
X-RAY DIFFRACTIONf_chiral_restr0.0841324
X-RAY DIFFRACTIONf_plane_restr0.0085429
X-RAY DIFFRACTIONf_dihedral_angle_d5.4434334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.25783060.28026030X-RAY DIFFRACTION92.11
1.13-1.140.26513170.26656129X-RAY DIFFRACTION92.84
1.14-1.160.28532840.25625990X-RAY DIFFRACTION92.13
1.16-1.170.26632760.25275981X-RAY DIFFRACTION91.05
1.17-1.190.25233050.24365985X-RAY DIFFRACTION89.72
1.19-1.20.24142870.2365863X-RAY DIFFRACTION89.1
1.2-1.220.24813310.23545989X-RAY DIFFRACTION91.63
1.22-1.240.24023610.22546101X-RAY DIFFRACTION94.14
1.24-1.260.23523490.22566123X-RAY DIFFRACTION93.73
1.26-1.280.24613550.2196260X-RAY DIFFRACTION94.99
1.28-1.30.22313080.20676285X-RAY DIFFRACTION95.94
1.3-1.320.19432940.19986265X-RAY DIFFRACTION95.42
1.32-1.350.19793170.19746313X-RAY DIFFRACTION95.6
1.35-1.380.1973780.18886213X-RAY DIFFRACTION94.98
1.38-1.410.20663550.19216180X-RAY DIFFRACTION94.92
1.41-1.440.19163390.17866220X-RAY DIFFRACTION95.06
1.44-1.480.20172940.17246246X-RAY DIFFRACTION94.52
1.48-1.520.1933030.16596093X-RAY DIFFRACTION93.3
1.52-1.560.16693350.15746128X-RAY DIFFRACTION92.86
1.56-1.610.17553560.15015971X-RAY DIFFRACTION91.95
1.61-1.670.17212810.14646008X-RAY DIFFRACTION90.88
1.67-1.730.16312690.14285812X-RAY DIFFRACTION88.14
1.73-1.810.14293590.14195976X-RAY DIFFRACTION92.09
1.81-1.910.14152640.13576205X-RAY DIFFRACTION93.44
1.91-2.030.13193020.12896126X-RAY DIFFRACTION92.72
2.03-2.180.13673190.12925955X-RAY DIFFRACTION90.93
2.19-2.40.15043190.12925982X-RAY DIFFRACTION91.37
2.4-2.750.13632920.13945518X-RAY DIFFRACTION83.84
2.75-3.470.14313490.14275691X-RAY DIFFRACTION87.75
3.47-28.590.15342970.14555783X-RAY DIFFRACTION88.06
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.31245144096-1.00702571647-1.101363967111.899106137740.6753715708191.93103934945-0.006574945025310.0130500239339-0.09329389503550.02406713044110.02970795220270.2173637044040.0229242948882-0.0925064992532-0.02407669290510.073792578955-0.010620313666-0.009156585787240.07356868130590.01012155883030.0871367354878-16.56025432386.77232015489-25.4302919988
20.423272389672-0.113225272643-0.1572220824760.77686492442-0.2669102937720.7498336355310.0119346977292-0.04845534907180.1828232651280.1617737800070.07796289700060.188651473101-0.107623449735-0.0589553262321-0.06463183094160.108872901080.01322289709190.01951151472550.09494842205960.0007297763702920.157120384452-14.869760386818.8862299577-17.3498424804
30.577882565698-0.0985049317621-0.01901722172980.459059849351-0.2794289651590.791572856474-0.0128154615399-0.02718446199430.02610751204960.02909278530240.04276725453280.05386717738820.0219714405493-0.0601433873362-0.03967414215410.08536239975160.0007010957767430.003348290241430.0719111369497-0.007727812964120.0826875558722-11.89132108178.58353724913-17.4687224233
40.1989418626920.0223580391810.09990313252020.600906484287-0.3773055099060.2999637444410.00345701255511-0.05638080574470.06809346715620.06441164830.0244087514615-0.0756923624534-0.06611367176710.0916747732648-0.02446503379830.0977762806770.00121792539954-0.007282158396190.112300782863-0.0244411838280.120065629178-2.1668181059813.7866988392-19.03685229
51.3896237057-0.2645124553090.7435335734570.519672502686-0.3169022951251.16252289504-0.075733144707-0.03172464364280.1266803569340.02637739711640.00662006997449-0.00943828841436-0.131835737064-0.02486892603230.04739568779630.102413904280.00228097838684-0.006855724029040.0873508581621-0.02092434425290.09829577998393.146084004645.33564182618-7.9456414276
61.863215035630.11236791890.3236777892590.4291068979890.1457050609080.382201204856-0.02720415548810.01568532584440.1072341521850.00237820548745-0.01852270708090.051128050306-0.000962159559838-0.03813170261340.04090040181640.07382422723930.001780093432520.002493086717990.0821536979843-0.00851984799080.0940498526349-0.644775492613-1.45216264464-12.1704339482
70.3837636449780.0678998128728-0.06847456763270.306193049306-0.1741611539550.1918177697570.01143289663280.0103025643358-0.046877131173-0.0232665774105-0.113320343311-0.0460844100958-0.08225236021310.04910737240840.07257494649510.1071484539580.00956967789581-0.003092896470670.1107485214980.0009348455045810.102727908509-1.8313001275-2.22872996273-24.6153036796
81.136855449510.170607129973-0.03531827785671.13016134267-0.3118043506251.08380759003-0.03049938781980.125546632992-0.0327097442285-0.0997297509640.0617861752895-0.02487613721330.0369852692871-0.0532876682561-0.02490896639150.07914308570185.73742736608E-50.001512456379930.101315306656-0.0009131145456980.086135452724813.3506067915-6.73991916134-18.8151500302
90.976329053816-0.03574450897210.01454094984710.6471601205740.2460734791440.476308326703-0.0111166545816-0.0718306624762-0.008864750163460.075822995792-0.00831362300020.02833118452840.0546359566119-0.02797425999230.02239945779020.0845594952558-0.004742542633890.002868163543850.0742521870540.001594657758240.0654297114942.58672572884-8.32853043464-5.66226795461
101.9661053732-0.346905752796-0.6354604249041.038770446160.1593574575670.774201382136-0.0793822357294-0.122937770819-0.182580217330.2151268508630.02004221704730.0591386364140.1262797635-0.00190323466460.08888317695880.142038951107-0.002347283594470.01199764229570.1007549161890.01335030683970.1020277356343.95583081126-16.4573034341-4.64480072544
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 17 )1 - 171 - 17
22chain 'A' and (resid 18 through 61 )18 - 6118 - 61
33chain 'A' and (resid 62 through 91 )62 - 9162 - 91
44chain 'A' and (resid 92 through 134 )92 - 13492 - 134
55chain 'A' and (resid 135 through 156 )135 - 156135 - 156
66chain 'A' and (resid 157 through 179 )157 - 179157 - 179
77chain 'A' and (resid 180 through 199 )180 - 199180 - 199
88chain 'A' and (resid 200 through 221 )200 - 221200 - 221
99chain 'A' and (resid 222 through 278 )222 - 278222 - 278
1010chain 'A' and (resid 279 through 298 )279 - 298279 - 298

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