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- PDB-3uau: Crystal structure of the lipoprotein JlpA -

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Basic information

Entry
Database: PDB / ID: 3uau
TitleCrystal structure of the lipoprotein JlpA
ComponentsSurface-exposed lipoprotein
KeywordsCELL ADHESION / adhesin / bacterial cell surface
Function / homologyAdhesin JlpA, Campylobacter / Adhesin from Campylobacter / cell adhesion / Surface-exposed lipoprotein / Surface-exposed lipoprotein
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKawai, F. / Yeo, H.J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structure of JlpA, a surface-exposed lipoprotein adhesin of Campylobacter jejuni.
Authors: Kawai, F. / Paek, S. / Choi, K.J. / Prouty, M. / Kanipes, M.I. / Guerry, P. / Yeo, H.J.
History
DepositionOct 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface-exposed lipoprotein
B: Surface-exposed lipoprotein


Theoretical massNumber of molelcules
Total (without water)86,7682
Polymers86,7682
Non-polymers00
Water00
1
A: Surface-exposed lipoprotein


Theoretical massNumber of molelcules
Total (without water)43,3841
Polymers43,3841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface-exposed lipoprotein


Theoretical massNumber of molelcules
Total (without water)43,3841
Polymers43,3841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.632, 111.632, 170.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Surface-exposed lipoprotein / JlpA


Mass: 43384.238 Da / Num. of mol.: 2 / Fragment: UNP residues 18-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: 81-176 / Gene: CJJ81176_1002, jlpA / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1VZX2, UniProt: A0A0H3P9U7*PLUS

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 32-36% MPD, 20-30 mM calcium chloride, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2009
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 27364 / % possible obs: 90.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.339 / % possible all: 76

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHARPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 35.145 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 0.784 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27221 1371 5 %RANDOM
Rwork0.24161 ---
obs0.24315 27356 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.289 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å20 Å20 Å2
2---4.68 Å2-0 Å2
3---9.35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 0 0 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225585
X-RAY DIFFRACTIONr_bond_other_d0.0010.023708
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.967523
X-RAY DIFFRACTIONr_angle_other_deg0.9339193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27627.526291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.421151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.402152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02995
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_it0.6581.53413
X-RAY DIFFRACTIONr_mcbond_other0.1131.51376
X-RAY DIFFRACTIONr_mcangle_it1.23325526
X-RAY DIFFRACTIONr_scbond_it1.76432172
X-RAY DIFFRACTIONr_scangle_it2.8974.51997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 76 -
Rwork0.378 1519 -
obs--100 %
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)
19.9453.64186.86146.28353.113610.77050.5535-0.3582-0.68991.1455-0.1385-0.12880.7142-0.3218-0.4150.63270.04710.00640.5862-0.00770.0544-15.189426.283131.5572
23.18381.45871.10667.34060.79333.6069-0.2970.3333-0.08280.020.2184-0.5867-0.15090.27290.07860.18210.03750.04320.345-0.03170.1772-5.900728.745920.3871
35.95321.8411.61647.96512.88292.0644-0.58181.1545-0.1065-0.17410.3936-1.2124-0.09770.64570.18810.3628-0.1830.14250.49850.19350.632813.542437.90712.1712
49.14453.7191-4.58033.6363-2.43649.79210.4219-0.581.11480.70930.04490.6008-0.59280.3015-0.46670.61090.03330.0020.6262-0.07150.1689-37.523742.149528.1292
53.05160.4589-0.88354.76460.30933.5463-0.1621-0.05150.1670.33680.04840.4685-0.01780.02670.11370.39160.07590.03790.51650.03660.068-48.886337.540521.823
63.92821.3926-0.96768.7674-3.46033.7253-0.2710.552-0.34250.40720.48291.97490.0481-0.8128-0.21180.1956-0.02510.15910.3547-0.06230.6876-69.093826.857411.0776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 107
2X-RAY DIFFRACTION2A108 - 236
3X-RAY DIFFRACTION3A237 - 367
4X-RAY DIFFRACTION4B17 - 70
5X-RAY DIFFRACTION5B71 - 237
6X-RAY DIFFRACTION6B247 - 366

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