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- PDB-1l7l: Crystal structure of Pseudomonas aeruginosa lectin 1 determined b... -

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Basic information

Entry
Database: PDB / ID: 1l7l
TitleCrystal structure of Pseudomonas aeruginosa lectin 1 determined by single wavelength anomalous scattering phasing method
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Pseudomonas aeruginosa / lectin / agglutinin / single wavelength anomalous scattering phasing / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.5 Å
AuthorsLiu, Z.J. / Tempel, W. / Lin, D. / Karaveg, K. / Doyle, R.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: AM.CRYST.ASSOC.,ABSTR.PAPERS (ANNUAL MEETING) / Year: 2002
Title: Structure determination of P. aeruginosa lectin-1 using single wavelength anomalous scattering data from native crystals (P028)
Authors: Liu, Z.J. / Tempel, W. / Lin, D. / Karaveg, K. / Doyle, R.J. / Rose, J.P. / Wang, B.C.
History
DepositionMar 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8102
Polymers12,7701
Non-polymers401
Water1,928107
1
A: PA-I galactophilic lectin
hetero molecules

A: PA-I galactophilic lectin
hetero molecules

A: PA-I galactophilic lectin
hetero molecules

A: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2418
Polymers51,0814
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)40.259, 72.351, 133.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe active tetramer is generated by applying the following transformations to deposited coordinates: -x,1-y,z; -x,y,-z; x,1-y,-z

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Components

#1: Protein PA-I galactophilic lectin / PA-IL / Galactose-binding lectin / lectin 1


Mass: 12770.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q05097
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 31830 / Num. obs: 31619 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.026 / Net I/σ(I): 61
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 10 / Num. unique all: 3029 / Rsym value: 0.14 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
SHELXmodel building
ISASmodel building
RESOLVEmodel building
CNS1.1refinement
SHELXphasing
ISASphasing
RESOLVEphasing
MAR345data collection
RefinementMethod to determine structure: SAS / Resolution: 1.5→14.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.793 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1535 5 %RANDOM
Rwork0.19225 ---
obs0.19262 29435 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.435 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.5→14.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 1 107 1005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021920
X-RAY DIFFRACTIONr_bond_other_d0.0020.02788
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9161257
X-RAY DIFFRACTIONr_angle_other_deg0.72231840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021066
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02176
X-RAY DIFFRACTIONr_nbd_refined0.20.2145
X-RAY DIFFRACTIONr_nbd_other0.2520.2874
X-RAY DIFFRACTIONr_nbtor_other0.0830.2514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.258
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7371.5594
X-RAY DIFFRACTIONr_mcangle_it1.3162950
X-RAY DIFFRACTIONr_scbond_it2.1693326
X-RAY DIFFRACTIONr_scangle_it3.3524.5307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 124
Rwork0.184 2025
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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