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- PDB-3rkp: Crystal structure of BcpA*(D312A), the major pilin subunit of Bac... -

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Basic information

Entry
Database: PDB / ID: 3rkp
TitleCrystal structure of BcpA*(D312A), the major pilin subunit of Bacillus cereus
ComponentsCollagen adhesion protein
KeywordsCELL ADHESION / intramolecular amide bond / jelly-roll / Ig / pilin subunit
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.243 Å
AuthorsHendrickx, A.P. / Poor, C.B. / Jureller, J.E. / Budzik, J.M. / He, C. / Schneewind, O.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus.
Authors: Hendrickx, A.P. / Poor, C.B. / Jureller, J.E. / Budzik, J.M. / He, C. / Schneewind, O.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,4672
Polymers78,4672
Non-polymers00
Water2,396133
1
A: Collagen adhesion protein


Theoretical massNumber of molelcules
Total (without water)39,2341
Polymers39,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagen adhesion protein


Theoretical massNumber of molelcules
Total (without water)39,2341
Polymers39,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.862, 68.096, 97.251
Angle α, β, γ (deg.)90.00, 107.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Collagen adhesion protein


Mass: 39233.578 Da / Num. of mol.: 2 / Fragment: unp residues 163-515 / Mutation: D312A, L182M, I261M, L357M, L426M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_2508 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81D71
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1M HEPES pH 7.5 20% PEG 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 41360 / Num. obs: 39085 / % possible obs: 94.5 % / Observed criterion σ(F): 2.24 / Observed criterion σ(I): 2.24 / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.96
Reflection shellResolution: 2.24→2.28 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.68 / % possible all: 61.3

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Processing

Software
NameVersionClassification
Blu-IceGUI (SSRL)data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KPT

3kpt


Resolution: 2.243→38.781 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 34.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1794 4.99 %random
Rwork0.2104 ---
obs0.2127 35971 87.09 %-
all-41303 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.213 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.5265 Å2-0 Å2-17.2745 Å2
2--6.1389 Å20 Å2
3---4.3876 Å2
Refinement stepCycle: LAST / Resolution: 2.243→38.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 0 133 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025518
X-RAY DIFFRACTIONf_angle_d0.5797462
X-RAY DIFFRACTIONf_dihedral_angle_d10.9632112
X-RAY DIFFRACTIONf_chiral_restr0.04869
X-RAY DIFFRACTIONf_plane_restr0.002953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2428-2.30350.423840.31091557X-RAY DIFFRACTION52
2.3035-2.37120.3992980.32581875X-RAY DIFFRACTION62
2.3712-2.44780.38991110.31552117X-RAY DIFFRACTION71
2.4478-2.53520.36471210.30252491X-RAY DIFFRACTION82
2.5352-2.63670.37611220.27652603X-RAY DIFFRACTION86
2.6367-2.75670.30561510.25072739X-RAY DIFFRACTION92
2.7567-2.9020.35871520.24542802X-RAY DIFFRACTION94
2.902-3.08370.29721580.24832883X-RAY DIFFRACTION96
3.0837-3.32170.31041520.24242962X-RAY DIFFRACTION98
3.3217-3.65580.2631480.22633003X-RAY DIFFRACTION99
3.6558-4.18420.23371550.18843032X-RAY DIFFRACTION100
4.1842-5.26960.19481760.14883033X-RAY DIFFRACTION100
5.2696-38.78680.18761660.17773080X-RAY DIFFRACTION99
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)
12.40110.221-0.03350.73560.01541.7062-0.0181-0.5753-0.128-0.03010.18620.43560.1595-0.1372-0.13520.40610.0757-0.19220.3415-0.14490.6094-89.5278-12.9144-33.1873
23.773-1.20061.39831.7808-0.75811.6885-0.0370.44690.3153-0.4016-0.1780.0886-0.02540.24380.17250.39430.08570.01260.2296-0.02430.2052-52.3647-18.0251-24.6753
32.61860.12690.96321.6055-0.3483.13310.30480.0996-0.58040.0129-0.188-0.18280.04820.3455-0.07510.1279-0.01320.05080.1117-0.00670.2295-20.0735-39.6734-1.1825
43.5843-1.12650.30311.0418-0.80271.1432-0.4584-1.5170.77870.45170.4729-0.3219-0.085-0.18330.05420.54350.133-0.41920.6764-0.05830.7701-74.216121.9343-35.3982
52.7784-0.91711.29781.8059-1.49351.9579-0.62930.17470.6613-0.21640.20520.1415-0.4612-0.30490.37270.54850.0379-0.1930.38430.00620.437-38.143812.8089-25.4761
65.1388-1.69420.53481.1840.1911.4949-0.1232-1.1893-0.7890.08910.1771-0.10120.00440.1305-0.08090.24420.07380.05820.56980.16860.51-8.9165-8.52491.6119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 166:267
2X-RAY DIFFRACTION2chain A and resseq 268:409
3X-RAY DIFFRACTION3chain A and resseq 410:515
4X-RAY DIFFRACTION4chain B and resseq 166:267
5X-RAY DIFFRACTION5chain B and resseq 268:409
6X-RAY DIFFRACTION6chain B and resseq 410:514

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