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- PDB-2vw8: Crystal Structure of Quinolone signal response protein pqsE from ... -

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Basic information

Entry
Database: PDB / ID: 2vw8
TitleCrystal Structure of Quinolone signal response protein pqsE from Pseudomonas aeruginosa
ComponentsPA1000
KeywordsSIGNALING PROTEIN / QUINOLONE SIGNAL RESPONSE PROTEIN / SSPF
Function / homology
Function and homology information


2-aminobenzoylacetyl-CoA thioesterase / secondary metabolite biosynthetic process / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / : / 2-aminobenzoylacetyl-CoA thioesterase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsCarter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Oke, M. / Naismith, J.H. / White, M.F.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili C, D. / Botting, H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionJun 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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_conn.ptnr2_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: PA1000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8055
Polymers34,4941
Non-polymers3114
Water3,153175
1
A: PA1000
hetero molecules

A: PA1000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,61010
Polymers68,9892
Non-polymers6218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3480 Å2
ΔGint-52.6 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.370, 57.690, 50.240
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PA1000 / PQSE


Mass: 34494.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P20581
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES AND LAST FOUR RESIDUES ARE DISORDERED

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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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6
Details: 40% PEG 400, 0.1M NA-CACODYLATE, PH6.0, 0.2M MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.737
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.737 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 51128 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.39
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.11 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.45→51.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.963 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18597 2616 5.1 %RANDOM
Rwork0.16613 ---
obs0.16713 48512 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.665 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.21 Å2
2--0.78 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 11 175 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212488
X-RAY DIFFRACTIONr_bond_other_d0.0020.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9673384
X-RAY DIFFRACTIONr_angle_other_deg0.88334166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99322.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23615419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7541531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.2210.2473
X-RAY DIFFRACTIONr_nbd_other0.1930.21864
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21188
X-RAY DIFFRACTIONr_nbtor_other0.0820.21361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8481.51965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93322407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.91231127
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6564.5972
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 191
Rwork0.194 3432
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)
10.96170.19180.12431.16240.18061.4462-0.0424-0.01550.06450.02560.04050.123-0.0931-0.16430.0019-0.08270.0042-0.0014-0.06630.0234-0.066521.96910.22913.876
21.51250.17730.22360.68890.16721.1424-0.02930.0295-0.26630.02860.0610.02250.1915-0.1078-0.0317-0.065-0.03-0.0019-0.08540.0094-0.069528.061-5.11410.158
31.34210.29780.0110.2431-0.06360.67870.0045-0.02170.02730.01920.0078-0.0397-0.0278-0.0055-0.0123-0.0735-0.0036-0.0102-0.0957-0.0094-0.085245.4768.0968.442
4115.973495.5138-11.341178.6637-9.34031.109-0.21991.10652.72721.31980.73910.4081-1.68091.0862-0.51920.01990.0120.0055-0.0293-0.03410.060836.557611.76713.7667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 135
2X-RAY DIFFRACTION2A136 - 178
3X-RAY DIFFRACTION3A179 - 297
4X-RAY DIFFRACTION4A401 - 403

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