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- PDB-2wfk: Calcium bound LipL32 -

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Basic information

Entry
Database: PDB / ID: 2wfk
TitleCalcium bound LipL32
ComponentsLIPL32
KeywordsMETAL BINDING PROTEIN / FIBRONECTIN / LIPOPROTEIN / CALCIUM BINDING / EXTRACELLULAR MATRIX OUTER MEMBRANE PROTEIN / CA2+-BOUND
Function / homologySurface lipoprotein of Spirochaetales order / Surface lipoprotein of Spirochaetales order / metal ion binding / LipL32
Function and homology information
Biological speciesLEPTOSPIRA SANTAROSAI SEROVAR SHERMANI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsTung, J.-Y. / Yang, C.-W. / Sun, Y.-J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Calcium Binds to Lipl32, a Lipoprotein from Pathogenic Leptospira, and Modulates Fibronectin Binding.
Authors: Tung, J.-Y. / Yang, C.-W. / Chou, S. / Lin, C. / Sun, Y.-J.
History
DepositionApr 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPL32
B: LIPL32
C: LIPL32
D: LIPL32
E: LIPL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,17010
Polymers143,9705
Non-polymers2005
Water9,512528
1
A: LIPL32
B: LIPL32
C: LIPL32
D: LIPL32
E: LIPL32
hetero molecules

A: LIPL32
B: LIPL32
C: LIPL32
D: LIPL32
E: LIPL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,34020
Polymers287,94010
Non-polymers40110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area27770 Å2
ΔGint-167.3 kcal/mol
Surface area96080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.905, 121.905, 206.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
LIPL32


Mass: 28793.953 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEPTOSPIRA SANTAROSAI SEROVAR SHERMANI (bacteria)
Plasmid: PRSETC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYS / References: UniProt: Q6S9S1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 55.42 % / Description: NONE
Crystal growDetails: TACSIMATE, PH7.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 69717 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 44.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 47.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 6.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→27.259 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 26.81 / Stereochemistry target values: ML
Details: DISORDERED REGIONS WERE MISSING FROM RESIUDE (B PRO 168 TO B THR 182), (C ILE 167 TO C ASN 179), (D ILE 165 TO D ILE 180)
RfactorNum. reflection% reflection
Rfree0.2618 3466 5.1 %
Rwork0.2189 --
obs0.221 68593 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.328 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.3425 Å20 Å20 Å2
2--2.3425 Å2-0 Å2
3----4.6851 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9335 0 5 528 9868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049569
X-RAY DIFFRACTIONf_angle_d0.90312983
X-RAY DIFFRACTIONf_dihedral_angle_d15.33550
X-RAY DIFFRACTIONf_chiral_restr0.0571411
X-RAY DIFFRACTIONf_plane_restr0.0031680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33150.33871290.26962492X-RAY DIFFRACTION96
2.3315-2.36480.3371390.26492526X-RAY DIFFRACTION97
2.3648-2.40010.31011080.25062573X-RAY DIFFRACTION98
2.4001-2.43750.31991470.25042555X-RAY DIFFRACTION98
2.4375-2.47750.25411510.23992528X-RAY DIFFRACTION98
2.4775-2.52020.29711410.24242532X-RAY DIFFRACTION98
2.5202-2.5660.33371180.24912591X-RAY DIFFRACTION98
2.566-2.61530.31381380.2582594X-RAY DIFFRACTION99
2.6153-2.66860.31451340.25322562X-RAY DIFFRACTION98
2.6686-2.72660.29961280.26052564X-RAY DIFFRACTION98
2.7266-2.790.29131330.2572579X-RAY DIFFRACTION98
2.79-2.85970.32451350.26482613X-RAY DIFFRACTION99
2.8597-2.93690.30181510.25822561X-RAY DIFFRACTION99
2.9369-3.02320.27421300.24142624X-RAY DIFFRACTION99
3.0232-3.12060.26191530.22682585X-RAY DIFFRACTION99
3.1206-3.2320.28251460.21452612X-RAY DIFFRACTION99
3.232-3.36120.23871470.20632615X-RAY DIFFRACTION99
3.3612-3.51390.23891460.20462630X-RAY DIFFRACTION99
3.5139-3.69870.22451500.20742501X-RAY DIFFRACTION94
3.6987-3.92980.2561450.20682630X-RAY DIFFRACTION99
3.9298-4.23220.2481410.20162640X-RAY DIFFRACTION99
4.2322-4.65620.21051370.18692682X-RAY DIFFRACTION100
4.6562-5.32560.22711450.18562720X-RAY DIFFRACTION100
5.3256-6.69320.23521330.21312760X-RAY DIFFRACTION100
6.6932-27.26070.2481410.20012858X-RAY DIFFRACTION98

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