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- PDB-3it5: Crystal Structure of the LasA Virulence Factor from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3it5
TitleCrystal Structure of the LasA Virulence Factor from Pseudomonas aeruginosa
ComponentsProtease lasA
KeywordsHYDROLASE / metallopeptidase / M23 / beta-protein / Cell membrane / Cell outer membrane / Membrane / Metal-binding / Metalloprotease / Protease / Zymogen
Function / homology
Function and homology information


protein transport by the Sec complex / protein secretion by the type II secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / peptidoglycan catabolic process / metalloendopeptidase activity / endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Peptidase M23A, B-lytic metalloendopeptidase / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSpencer, J. / Murphy, L.M. / Conners, R. / Sessions, R.B. / Gamblin, S.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the LasA virulence factor from Pseudomonas aeruginosa: substrate specificity and mechanism of M23 metallopeptidases.
Authors: Spencer, J. / Murphy, L.M. / Conners, R. / Sessions, R.B. / Gamblin, S.J.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease lasA
B: Protease lasA
E: Protease lasA
G: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1858
Polymers79,9244
Non-polymers2624
Water13,205733
1
A: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0462
Polymers19,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0462
Polymers19,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0462
Polymers19,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0462
Polymers19,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.818, 34.079, 105.837
Angle α, β, γ (deg.)90.000, 102.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 3 - 180 / Label seq-ID: 3 - 180

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3EC
4GD

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Components

#1: Protein
Protease lasA / Staphylolytic protease


Mass: 19980.902 Da / Num. of mol.: 4 / Fragment: UNP residues 237-418 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1
References: UniProt: P14789, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 277 K / pH: 7
Details: 50mM TrisCl 100mM NaCl, pH 7.0, spontaneous crystallization, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.01→20 Å / Num. obs: 48468 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.062 / Χ2: 1.088 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.0830.11944531.193190.7
2.08-2.173.30.10548001.205196.5
2.17-2.263.20.09548111.174196
2.26-2.383.30.08747881.147197.3
2.38-2.533.30.07948821.084197.4
2.53-2.733.30.07348871.093197.6
2.73-33.30.06248821.061197.1
3-3.433.20.05649381.027197.4
3.43-4.323.20.05149120.998196.7
4.32-203.10.04851150.917197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.828 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.804 / SU B: 13.35 / SU ML: 0.178 / SU R Cruickshank DPI: 0.253 / SU Rfree: 0.358 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1194 4.9 %RANDOM
Rwork0.186 ---
obs0.19 24166 47.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.34 Å2 / Biso mean: 7.852 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.65 Å2
2---0.47 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 4 733 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215828
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9047977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93922.917288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26315745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8381536
X-RAY DIFFRACTIONr_chiral_restr0.0780.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214736
X-RAY DIFFRACTIONr_mcbond_it0.2471.53589
X-RAY DIFFRACTIONr_mcangle_it0.44825730
X-RAY DIFFRACTIONr_scbond_it0.65732239
X-RAY DIFFRACTIONr_scangle_it1.0514.52246
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1384 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.330.5
BMEDIUM POSITIONAL0.30.5
EMEDIUM POSITIONAL0.330.5
GMEDIUM POSITIONAL0.330.5
AMEDIUM THERMAL0.22
BMEDIUM THERMAL0.192
EMEDIUM THERMAL0.192
GMEDIUM THERMAL0.192
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 79 -
Rwork0.198 1482 -
all-1561 -
obs--44.28 %
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)
10.1448-0.0835-0.00050.5439-0.03620.1486-0.0073-0.0129-0.00380.0380.026-0.0016-0.00130.0121-0.01870.02510.0033-0.01570.01910.00250.014843.12-0.31415.257
20.4365-0.0655-0.01960.4042-0.0130.2172-0.00680.0034-0.0010.03210.020.02120.0110.0069-0.01320.0172-0.0052-0.01070.01420.00720.011724.9080.1858.149
30.4440.0918-0.07360.49550.00720.2240.0034-0.0353-0.01130.0107-0.01470.00980.01-0.02120.01120.01810.0002-0.01240.02390.00580.01466.9420.314109.743
40.0981-0.0558-0.07630.6617-0.01670.33060.01890.0070.0128-0.00420.0030.0159-0.0192-0.0311-0.02190.01340.0056-0.0080.02570.00520.017785.164-0.18966.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2B1 - 181
3X-RAY DIFFRACTION3E2 - 182
4X-RAY DIFFRACTION4G2 - 181

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