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- PDB-2zz8: Crystal structure of LipL32, the most abundant surface protein of... -

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Basic information

Entry
Database: PDB / ID: 2zz8
TitleCrystal structure of LipL32, the most abundant surface protein of pathogenic leptospira spp
ComponentsLipL32 protein
KeywordsUNKNOWN FUNCTION / Leptospira / outer-membrane protein
Function / homologySurface lipoprotein of Spirochaetales order / Surface lipoprotein of Spirochaetales order / Prokaryotic membrane lipoprotein lipid attachment site profile. / LipL32
Function and homology information
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsVivian, J.P. / Beddoe, T. / Rossjohn, J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of LipL32, the most abundant surface protein of pathogenic Leptospira spp.
Authors: Vivian, J.P. / Beddoe, T. / McAlister, A.D. / Wilce, M.C. / Zaker-Tabrizi, L. / Troy, S. / Byres, E. / Hoke, D.E. / Cullen, P.A. / Lo, M. / Murray, G.L. / Adler, B. / Rossjohn, J.
History
DepositionFeb 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LipL32 protein
B: LipL32 protein


Theoretical massNumber of molelcules
Total (without water)52,9602
Polymers52,9602
Non-polymers00
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-25 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.895, 125.895, 95.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LipL32 protein


Mass: 26480.059 Da / Num. of mol.: 2 / Fragment: residues in database 21-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Strain: Lai / Gene: lipl32 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O34094
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.0M sodium malonate, 0.1M sodium cacodylate, 4%(v/v) butyrolactone, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
SYNCHROTRONAustralian Synchrotron MX120.954
Detector
TypeIDDetectorDetails
RIGAKU RAXIS IV++1IMAGE PLATEmirrors
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9541
ReflectionResolution: 2→40 Å / Num. all: 59453 / Num. obs: 59453 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21.4 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.08 / Net I/σ(I): 41.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→37.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.207 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 2969 5.1 %RANDOM
Rwork0.1813 ---
obs0.1831 55681 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 0 435 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9864952
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06424.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91315600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.481514
X-RAY DIFFRACTIONr_chiral_restr0.110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222760
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.691.52300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24723732
X-RAY DIFFRACTIONr_scbond_it1.9531340
X-RAY DIFFRACTIONr_scangle_it3.1324.51220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 184 -
Rwork0.329 3866 -
obs--93.71 %
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)
11.7458-0.56580.07883.1734-0.18983.20090.0162-0.02940.1091-0.0722-0.0330.167-0.1257-0.05860.01690.0725-0.06870.01420.0665-0.0230.066-9.65573.3257.451
24.01281.7641.64052.35890.90552.77280.2026-0.1693-0.13820.051-0.18570.08040.0609-0.0884-0.0170.2247-0.12130.05240.1621-0.00610.1263-27.21147.3849.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 242
2X-RAY DIFFRACTION2B6 - 242

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