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- PDB-3kpt: Crystal structure of BcpA, the major pilin subunit of Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 3kpt
TitleCrystal structure of BcpA, the major pilin subunit of Bacillus cereus
ComponentsCollagen adhesion protein
KeywordsCELL ADHESION / Intramolecular Amide Bond / Pilin Subunit / Beta Sheet
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen adhesion protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.102 Å
AuthorsPoor, C.B. / Budzik, J.M. / Schneewind, O. / He, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Intramolecular amide bonds stabilize pili on the surface of bacilli.
Authors: Budzik, J.M. / Poor, C.B. / Faull, K.F. / Whitelegge, J.P. / He, C. / Schneewind, O.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 25, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_distant_solvent_atoms ...database_2 / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 13, 2021Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen adhesion protein
B: Collagen adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9703
Polymers78,9302
Non-polymers401
Water4,071226
1
A: Collagen adhesion protein


Theoretical massNumber of molelcules
Total (without water)39,4651
Polymers39,4651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagen adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5052
Polymers39,4651
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.552, 73.862, 201.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Collagen adhesion protein


Mass: 39465.164 Da / Num. of mol.: 2 / Fragment: UNP residues 163-515 / Mutation: L182M, I261M, L357M, L426M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: bcpA, BC_2508 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81D71
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Calcium acetate, 0.05M Tris-HCl pH 7.5, 0.15M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97929, 0.97946, 0.96863
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2009
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979461
30.968631
ReflectionResolution: 2.1→50 Å / Num. all: 48052 / Num. obs: 48052 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.14 Å / % possible all: 57.7

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.102→41.6066 Å / SU ML: 0.38 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 1944 4.16 %random
Rwork0.2308 ---
all0.2327 46778 --
obs0.2327 46778 85.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.092 Å2 / ksol: 0.321 e/Å3
Refinement stepCycle: LAST / Resolution: 2.102→41.6066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 1 226 5708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035569
X-RAY DIFFRACTIONf_angle_d0.6997500
X-RAY DIFFRACTIONf_dihedral_angle_d14.2692101
X-RAY DIFFRACTIONf_chiral_restr0.047875
X-RAY DIFFRACTIONf_plane_restr0.003958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.15460.3291780.28211953X-RAY DIFFRACTION53
2.1546-2.21280.3892920.27432164X-RAY DIFFRACTION59
2.2128-2.27790.3462990.28412342X-RAY DIFFRACTION64
2.2779-2.35140.34491130.28752618X-RAY DIFFRACTION71
2.3514-2.43550.37791240.27992914X-RAY DIFFRACTION79
2.4355-2.5330.33721400.27583169X-RAY DIFFRACTION86
2.533-2.64820.31621470.28453394X-RAY DIFFRACTION92
2.6482-2.78780.35191640.29133616X-RAY DIFFRACTION98
2.7878-2.96250.36111620.29453695X-RAY DIFFRACTION100
2.9625-3.19110.36341590.27213721X-RAY DIFFRACTION100
3.1911-3.51210.28371620.25183729X-RAY DIFFRACTION100
3.5121-4.020.27341650.21723753X-RAY DIFFRACTION100
4.02-5.06330.22381660.16933803X-RAY DIFFRACTION100
5.0633-41.60660.20051730.19073963X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.8208-0.73230.32022.4081-0.47322.7743-0.0514-0.0237-0.1344-0.20760.06690.1487-0.2625-0.7511-0.02830.18250.03640.01370.29030.00060.21530.841134.641962.7006
22.18670.0881-1.5996-0.0108-0.80484.505-0.13580.1624-0.0146-0.2806-0.0632-0.08480.37520.43590.18330.47940.03820.11890.180.03020.2242
32.7108-0.1138-1.1811.1898-0.33021.8063-0.43470.3925-0.1723-0.02490.0702-0.01851.3295-0.98330.31011.0953-0.13380.21330.5157-0.08380.3003
43.16370.0382-1.58392.5911-1.78374.0990.09790.32180.0343-0.2866-0.08620.0157-0.8295-0.3588-0.11130.2089-0.05740.06820.0819-0.02430.0747
53.59880.21642.19491.19241.1936.1890.9842-0.1174-0.31110.8951-0.3318-0.05072.11540.2825-0.58520.9050.1078-0.17340.3115-0.07090.2492
60.39491.29511.64093.2548-0.18272.88190.18380.694-0.3851-0.27590.4208-0.29510.65061.4772-0.43360.44780.4956-0.13820.8944-0.28680.2777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 141:242A141 - 242
2X-RAY DIFFRACTION2chain A and resseq 243:384A243 - 384
3X-RAY DIFFRACTION3chain A and resseq 385:490A385 - 490
4X-RAY DIFFRACTION4chain B and resseq 136:242B136 - 242
5X-RAY DIFFRACTION5chain B and resseq 243:384B243 - 384
6X-RAY DIFFRACTION6chain B and resseq 385:490B385 - 490

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