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- PDB-3qq2: Crystal Structure of the Beta Domain of the Bordetella Autotransp... -

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Basic information

Entry
Database: PDB / ID: 3qq2
TitleCrystal Structure of the Beta Domain of the Bordetella Autotransporter Brka
ComponentsBrkA autotransporter
KeywordsMEMBRANE PROTEIN/PROTEIN TRANSPORT / BETA BARREL / TRANSMEMBRANE / MEMBRANE PROTEIN-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


cell outer membrane / periplasmic space / cell surface / extracellular region
Similarity search - Function
Pertactin virulence factor family / Pertactin, central region / Pertactin / : / Autotransporter beta-domain / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain ...Pertactin virulence factor family / Pertactin, central region / Pertactin / : / Autotransporter beta-domain / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BrkA autotransporter
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhai, Y. / Zhang, K. / Huo, Y. / Sun, F.
CitationJournal: Biochem.J. / Year: 2011
Title: Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the beta-domain pore
Authors: Zhai, Y. / Zhang, K. / Huo, Y. / Zhu, Y. / Zhou, Q. / Lu, J. / Black, I. / Pang, X. / Roszak, A.W. / Zhang, X. / Isaacs, N.W. / Sun, F.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: BrkA autotransporter
B: BrkA autotransporter
C: BrkA autotransporter


Theoretical massNumber of molelcules
Total (without water)92,9653
Polymers92,9653
Non-polymers00
Water00
1
A: BrkA autotransporter

A: BrkA autotransporter


Theoretical massNumber of molelcules
Total (without water)61,9772
Polymers61,9772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2700 Å2
ΔGint-11 kcal/mol
Surface area25680 Å2
MethodPISA
2
B: BrkA autotransporter
C: BrkA autotransporter


Theoretical massNumber of molelcules
Total (without water)61,9772
Polymers61,9772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-9 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.510, 122.372, 405.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BrkA autotransporter / Serum resistance protein BrkA / BrkA translocator


Mass: 30988.332 Da / Num. of mol.: 3 / Fragment: BETA DOMAIN, UNP RESIDUES 727-1010 / Mutation: L727M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: BP3494, brkA / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q45340

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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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100MM TIS-HCL, 10MM SPERMIDINE, 200MM LICL, 25% PEG 2000, PH8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07176 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07176 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. all: 30635 / Num. obs: 29563 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 97.3 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 35.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.268 / % possible all: 75

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QOM

2qom


Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.848 / SU B: 41.812 / SU ML: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1507 5.1 %RANDOM
Rwork0.266 ---
all0.269 30552 --
obs0.269 28054 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---2.22 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 0 0 5772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215927
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9298012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80921.528301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.5115850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571571
X-RAY DIFFRACTIONr_chiral_restr0.1090.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024768
X-RAY DIFFRACTIONr_mcbond_it0.4711.53619
X-RAY DIFFRACTIONr_mcangle_it0.92225629
X-RAY DIFFRACTIONr_scbond_it1.31932308
X-RAY DIFFRACTIONr_scangle_it2.3144.52383
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 94 -
Rwork0.383 1474 -
obs--72.29 %
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)
11.8190.1475-0.12892.3669-1.03652.17660.15760.0726-0.0626-0.2016-0.09580.0960.4335-0.2959-0.06180.2399-0.129-0.10430.11860.03980.156316.663-7.293729.0123
21.4092-0.0694-0.04863.7527-0.7672.0759-0.2155-0.27440.20630.2250.0294-0.0774-0.29660.23210.18610.2517-0.1674-0.09540.27870.05520.1766.269-40.996441.6166
32.21830.07381.49670.7964-0.46784.47840.0112-0.40420.07830.00810.063-0.02860.23290.0536-0.07420.47790.0657-0.10290.89080.01410.4836.95-68.410984.1491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A745 - 1010
2X-RAY DIFFRACTION2B745 - 1010
3X-RAY DIFFRACTION3C745 - 1010

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