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- PDB-2xg5: E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilu... -

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Basic information

Entry
Database: PDB / ID: 2xg5
TitleE. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 5d
Components
  • CHAPERONE PROTEIN PAPD
  • PAP FIMBRIAL MINOR PILIN PROTEIN
KeywordsCHAPERONE / CHAPERONE-SURFACE ACTIVE PROTEIN COMPLEX
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / cell wall organization / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-EC2 / Chem-EC5 / S-1,2-PROPANEDIOL / PAP fimbrial minor pilin protein / Chaperone protein PapD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRemaut, H. / Phan, G. / Buelens, F. / Chorell, E. / Pinkner, J.S. / Edvinsson, S. / Almqvist, F. / Hultgren, S.J. / Waksman, G.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Design and Synthesis of C-2 Substituted Thiazolo and Dihydrothiazolo Ring-Fused 2-Pyridones: Pilicides with Increased Antivirulence Activity.
Authors: Chorell, E. / Pinkner, J.S. / Phan, G. / Edvinsson, S. / Buelens, F. / Remaut, H. / Waksman, G. / Hultgren, S.J. / Almqvist, F.
History
DepositionMay 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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 / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN PAPD
B: PAP FIMBRIAL MINOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0407
Polymers43,8882
Non-polymers1,1525
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-9.8 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.610, 149.830, 82.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1175-

CO

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CHAPERONE PROTEIN PAPD / PAPD


Mass: 24589.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL 6XHIS TAG / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P15319
#2: Protein PAP FIMBRIAL MINOR PILIN PROTEIN / PAPH


Mass: 19297.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL RESIDUES 1-22 DELETED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P07111

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Non-polymers , 6 types, 207 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EC2 / (2R,3R)-8-CYCLOPROPYL-7-(NAPHTHALEN-1-YLMETHYL)-5-OXO-2-PHENYL-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID


Mass: 453.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H23NO3S
#5: Chemical ChemComp-EC5 / (2R)-2-[5-CYCLOPROPYL-6-(HYDROXYSULFANYL)-4-(NAPHTHALEN-1-YLMETHYL)-2-OXOPYRIDIN-1(2H)-YL]-3-PHENYLPROPANOIC ACID


Mass: 471.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H25NO4S
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details- (EC5): RADIOLYSIS PRODUCT OF EC2

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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: 3.7 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 6.5
Details: 0.01 M COBALT CHLORIDE, 0.1 M MES PH 6.5 AND 1.8 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 37302 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J2Z

2j2z


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.909 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS FOR WHICH NO DENSITY IS OBSERVED ARE MODELED WITH AS LIKELY CONFORMER AND WITH OCCUPANCY SET TO 0.01 ATOM RECORD. CONTAINS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS FOR WHICH NO DENSITY IS OBSERVED ARE MODELED WITH AS LIKELY CONFORMER AND WITH OCCUPANCY SET TO 0.01 ATOM RECORD. CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21503 1970 5 %RANDOM
Rwork0.18928 ---
obs0.19059 37302 89.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.909 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 79 202 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8282.0014054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73223.91133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4291525
X-RAY DIFFRACTIONr_chiral_restr0.1540.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212297
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.51827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32622951
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1931147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9934.51091
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: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 159 -
Rwork0.179 2780 -
obs--92.57 %
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)
11.2369-0.66971.07490.8763-1.21533.0082-0.0216-0.1825-0.06090.14360.0692-0.11170.25570.2281-0.04770.2130.11-0.03990.1814-0.02150.1669-34.735-24.79710.544
20.946-0.2731-0.79861.6196-0.27282.9750.0486-0.03820.10360.00290.0116-0.0274-0.07730.046-0.06010.0063-0.0008-0.00230.0275-0.00920.0609-43.498-10.151-3.18
32.3532-1.4681-0.78673.43260.63711.8240.06650.0579-0.0175-0.0888-0.0102-0.35390.16770.2765-0.05630.07930.06030.02750.1361-0.01140.1151-28.921-25.865-21.759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B25 - 173
2X-RAY DIFFRACTION2A1 - 119
3X-RAY DIFFRACTION3A120 - 216

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