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- PDB-3frl: The 2.25 A crystal structure of LipL32, the major surface antigen... -

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Basic information

Entry
Database: PDB / ID: 3frl
TitleThe 2.25 A crystal structure of LipL32, the major surface antigen of Leptospira interrogans serovar Copenhageni
ComponentsLipL32
KeywordsMEMBRANE PROTEIN / core jelly-roll fold
Function / homologySurface lipoprotein of Spirochaetales order / Surface lipoprotein of Spirochaetales order / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2,2',2''-NITRILOTRIETHANOL / OXALATE ION / LipL32
Function and homology information
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsFarah, C.S. / Guzzo, C.R. / Hauk, P. / Ho, P.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and calcium-binding activity of LipL32, the major surface antigen of pathogenic Leptospira sp.
Authors: Hauk, P. / Guzzo, C.R. / Roman Ramos, H. / Ho, P.L. / Farah, C.S.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LipL32
B: LipL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9986
Polymers55,6382
Non-polymers3614
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-18 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.725, 126.725, 95.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-279-

HOH

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Components

#1: Protein LipL32


Mass: 27818.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Strain: str. Fiocruz L1-130 / Gene: LIC11352, LIC_11352, lipL32 / Plasmid: pAE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(SI) / References: UniProt: Q72SM7
#2: Chemical ChemComp-211 / 2,2',2''-NITRILOTRIETHANOL


Mass: 149.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO3
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 1.4 M trisodium citrate, 0.1 M HEPES, 20 mM triethanolamine-HCl, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459, 0.97814, 0.97831
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4591
20.978141
30.978311
ReflectionResolution: 2.25→40 Å / Num. all: 42419 / Num. obs: 42419 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 22
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.968 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22712 2129 5 %RANDOM
Rwork0.18134 ---
obs0.18358 40149 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å21.17 Å20 Å2
2--2.33 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 23 272 3919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223737
X-RAY DIFFRACTIONr_bond_other_d0.0030.022602
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9935070
X-RAY DIFFRACTIONr_angle_other_deg0.92536402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00524.83147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98915641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4641514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_nbd_refined0.1970.2765
X-RAY DIFFRACTIONr_nbd_other0.2070.22646
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21739
X-RAY DIFFRACTIONr_nbtor_other0.090.21989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.050.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.29
X-RAY DIFFRACTIONr_mcbond_it0.8021.52796
X-RAY DIFFRACTIONr_mcbond_other0.1791.5928
X-RAY DIFFRACTIONr_mcangle_it1.1223791
X-RAY DIFFRACTIONr_scbond_it1.76431639
X-RAY DIFFRACTIONr_scangle_it2.2374.51278
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 159 -
Rwork0.278 2814 -
obs--95.53 %

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