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- PDB-2xg4: E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilu... -

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Basic information

Entry
Database: PDB / ID: 2xg4
TitleE. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 2c
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-XC2 / PAP fimbrial minor pilin protein / Chaperone protein PapD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)44,5155
Polymers43,8882
Non-polymers6283
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-9.3 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.100, 148.730, 82.639
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-1174-

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 REMOVED. / 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 , 4 types, 86 molecules

#3: Chemical ChemComp-XC2 / (3R)-8-CYCLOPROPYL-6-(MORPHOLIN-4-YLMETHYL)-7-(1-NAPHTHYLMETHYL)-5-OXO-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID


Mass: 476.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N2O4S
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 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: ESRF / Beamline: ID29 / Wavelength: 0.98023
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98023 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 24104 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7.3 / % possible all: 99.6

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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: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.131 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.185 / 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
Rfree0.21745 1290 5.1 %RANDOM
Rwork0.18332 ---
obs0.18508 22814 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.692 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 41 83 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9813934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63523.969131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60315464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2571524
X-RAY DIFFRACTIONr_chiral_restr0.1390.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212233
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_it1.0961.51819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04522928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.58131072
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8934.51003
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: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 89 -
Rwork0.209 1744 -
obs--99.3 %
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)
11.25750.327-1.33560.933-0.27582.9564-0.04750.101-0.0104-0.13970.0759-0.0499-0.24050.1935-0.02840.0967-0.09050.01730.0942-0.01070.054216.95624.823-10.227
20.84380.19651.02221.3433-0.85223.69910.03050.0057-0.118-0.03340.04890.00310.14840.0242-0.07930.0292-0.0034-0.00350.0071-0.00460.05888.32710.2163.541
31.83421.32430.83522.66790.90161.48950.0144-0.0239-0.05230.13660.0434-0.1718-0.13080.2134-0.05790.0705-0.0552-0.03580.0876-0.00490.047622.84125.67821.771
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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