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- PDB-3gi1: Crystal Structure of the laminin-binding protein Lbp of Streptoco... -

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Basic information

Entry
Database: PDB / ID: 3gi1
TitleCrystal Structure of the laminin-binding protein Lbp of Streptococcus pyogenes
ComponentsLaminin-binding protein of group A streptococci
KeywordsMETAL TRANSPORT / zinc-binding receptor / metal-binding / helical backbone / alpha/beta domains / laminin-binding protein / Lbp / Transport
Function / homology
Function and homology information


zinc ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Laminin-binding protein of group A streptococci / Laminin adhesion
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsLinke, C. / Caradoc-Davies, T.T. / Young, P.G. / Proft, T. / Baker, E.N.
CitationJournal: J.Bacteriol. / Year: 2009
Title: The laminin-binding protein Lbp from Streptococcus pyogenes is a zinc receptor
Authors: Linke, C. / Caradoc-Davies, T.T. / Young, P.G. / Proft, T. / Baker, E.N.
History
DepositionMar 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Laminin-binding protein of group A streptococci
B: Laminin-binding protein of group A streptococci
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9514
Polymers63,8202
Non-polymers1312
Water1,42379
1
A: Laminin-binding protein of group A streptococci
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9752
Polymers31,9101
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Laminin-binding protein of group A streptococci
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9752
Polymers31,9101
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.624, 92.163, 70.614
Angle α, β, γ (deg.)90.000, 106.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Laminin-binding protein of group A streptococci / Lbp


Mass: 31910.070 Da / Num. of mol.: 2 / Fragment: UNP residues 24-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: serotype M1 SF370 / Gene: lmb, lmb/spy_2007 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DII5, UniProt: Q99XV3*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.09 Å3/Da / Density % sol: 41.04 % / Mosaicity: 1.32 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.7ul of 37 mg/ml Lbp in PBS, pH7.4 + 0.002% Na-azide + 0.7ul of 30% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR345DTB / Detector: IMAGE PLATE / Date: Aug 20, 2007 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→27.984 Å / Num. all: 20587 / Num. obs: 20587 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.861
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.537.20.5971.22162730040.597100
2.53-2.687.30.4221.82060128370.422100
2.68-2.877.30.2862.71941626690.286100
2.87-3.17.30.1754.21801924650.175100
3.1-3.397.30.1146.51679322860.114100
3.39-3.797.40.0858.51528320770.085100
3.79-4.387.40.06311.21351218280.063100
4.38-5.377.40.05512.61144815480.055100
5.37-7.597.40.05812.1884012000.058100
7.59-29.097.10.04213.947716730.04297.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.98 Å
Translation2.5 Å27.98 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.33data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8

1toa

1k0f

1pq4

1xvl

2o1e

3hh8


Resolution: 2.45→27.982 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.42 / σ(F): 1.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.251 1947 5.14 %
Rwork0.186 --
obs0.19 20569 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.216 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 78.73 Å2 / Biso mean: 39.498 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1-7.381 Å20 Å27.209 Å2
2---5.336 Å2-0 Å2
3----2.045 Å2
Refinement stepCycle: LAST / Resolution: 2.45→27.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 2 79 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153996
X-RAY DIFFRACTIONf_angle_d1.565423
X-RAY DIFFRACTIONf_chiral_restr0.103622
X-RAY DIFFRACTIONf_plane_restr0.008697
X-RAY DIFFRACTIONf_dihedral_angle_d18.1631402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.5110.3361450.2472599274499.85
2.511-2.5790.2721240.23225672691100
2.579-2.6550.2981200.20826162736100
2.655-2.7410.3031170.20425552672100
2.741-2.8390.2571450.20725892734100
2.839-2.9520.3411550.2142542269799.96
2.952-3.0860.3321450.222556270199.93
3.086-3.2490.2961520.22325612713100
3.249-3.4520.2841400.1992544268499.93
3.452-3.7180.2621380.1772567270599.93
3.718-4.0910.2161320.14925642696100
4.091-4.6810.1721220.14126232745100
4.681-5.8880.2061490.14525472696100
5.888-27.9830.21630.1642534269799.85

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