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- PDB-4b0m: Complex of the Caf1AN usher domain, Caf1M chaperone and Caf1 subu... -

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Basic information

Entry
Database: PDB / ID: 4b0m
TitleComplex of the Caf1AN usher domain, Caf1M chaperone and Caf1 subunit from Yersinia pestis
Components
  • CHAPERONE PROTEIN CAF1M
  • F1 CAPSULE ANTIGEN
  • F1 CAPSULE-ANCHORING PROTEIN
KeywordsPROTEIN TRANSPORT / CHAPERONE-USHER PATHWAY / PILI ASSEMBLY
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / capsule / pilus / : / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / extracellular region
Similarity search - Function
PapC, N-terminal domain / F1 capsule antigen / Caf1 Capsule antigen / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein ...PapC, N-terminal domain / F1 capsule antigen / Caf1 Capsule antigen / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / 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 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chaperone protein caf1M / F1 capsule antigen / F1 capsule-anchoring protein
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDubnovitsky, A. / Yu, X.D. / Pudney, A.F. / MacIntyre, S. / Knight, S.D. / Zavialov, A.V.
CitationJournal: Structure / Year: 2012
Title: Allosteric Mechanism Controls Traffic in the Chaperone/Usher Pathway.
Authors: Di Yu, X. / Dubnovitsky, A. / Pudney, A.F. / Macintyre, S. / Knight, S.D. / Zavialov, A.V.
History
DepositionJul 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 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: F1 CAPSULE-ANCHORING PROTEIN
B: F1 CAPSULE ANTIGEN
M: CHAPERONE PROTEIN CAF1M


Theoretical massNumber of molelcules
Total (without water)57,2913
Polymers57,2913
Non-polymers00
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-32 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.281, 77.436, 95.858
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein F1 CAPSULE-ANCHORING PROTEIN


Mass: 15386.396 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P26949
#2: Protein F1 CAPSULE ANTIGEN


Mass: 15575.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P26948
#3: Protein CHAPERONE PROTEIN CAF1M / CAPSULE PROTEIN FRACTION 1


Mass: 26329.012 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P26926
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: HANGING DROPS OF 1.5 UL CAF1AN:CAF1M:CAF1 COMPLEX (35 MG/ML) PLUS 1.5 UL OF 15% PEG 3350, 0.1 M NA-CACODYLATE, PH 6.4, 1-2 WEEKS AT 6 DEG C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 47312 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5V

1p5v


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.387 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2310 5.02 %RANDOM
Rwork0.1833 ---
obs0.186 45816 96.867 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.777 Å2
Baniso -1Baniso -2Baniso -3
1-1.296 Å20 Å2-1.956 Å2
2---1.401 Å20 Å2
3----0.471 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 0 429 4095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9685098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75325.528161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83315614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2751511
X-RAY DIFFRACTIONr_chiral_restr0.1420.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022835
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21533
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22481
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.52443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96423832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68631510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0014.51266
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 133 -
Rwork0.258 2529 -
obs--76.101 %
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)
10.20720.06480.11290.76850.09670.6371-0.0115-0.10960.0336-0.1430.03120.09420.0030.043-0.0197-0.1029-0.01170.0218-0.04810.0091-0.0915-1.6393.42623.489
20.4579-0.22650.0983.0051.68292.95040.07030.1227-0.0180.02080.1096-0.06070.4880.151-0.180.08990.03-0.0613-0.1435-0.0247-0.14491.543-17.7617.708
30.9201-0.45111.31740.8217-0.86072.41060.0989-0.102-0.0432-0.1328-0.0035-0.00170.3046-0.0143-0.0954-0.0855-0.0050.0108-0.07510.0111-0.1067.303-10.16737.315
42.4341.24730.57816.76950.00795.5444-0.1149-0.21270.47370.14520.0051-0.1167-0.42370.0330.1098-0.1486-0.00680.0004-0.0399-0.0566-0.07741.51115.13635.4
55.7199-3.38083.25473.7336-0.98744.84240.19930.0281-0.2367-0.5117-0.31040.4495-0.4461-0.25880.111-0.03580.1246-0.1137-0.1062-0.0839-0.0517-16.83428.8720.601
624.9108-3.1091-17.31211.5951-1.340330.18640.30731.4938-0.4280.6939-0.29550.2744-0.09040.7269-0.0118-0.00180.02440.0101-0.0175-0.0545-0.028-37.17528.68413.284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1M4 - 56
2X-RAY DIFFRACTION1M59 - 106
3X-RAY DIFFRACTION1M123 - 147
4X-RAY DIFFRACTION2M148 - 235
5X-RAY DIFFRACTION3B15 - 149
6X-RAY DIFFRACTION4A1 - 9
7X-RAY DIFFRACTION5A30 - 121
8X-RAY DIFFRACTION6A122 - 135

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