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- PDB-4h0f: Mutant Structure of laminin-binding adhesin (Lmb) from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 4h0f
TitleMutant Structure of laminin-binding adhesin (Lmb) from Streptococcus agalactiae
ComponentsLaminin-binding surface protein
KeywordsCELL ADHESION / Adhesin / Human Laminin
Function / homology
Function and homology information


metal 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Laminin-binding surface protein
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKarthe, P. / Preethi, R.
CitationJournal: Plos One / Year: 2013
Title: Metal binding is critical for the folding and function of laminin binding protein, Lmb of Streptococcus agalactiae.
Authors: Ragunathan, P. / Sridaran, D. / Weigel, A. / Shabayek, S. / Spellerberg, B. / Ponnuraj, K.
History
DepositionSep 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Jul 29, 2015Group: Other
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_label_asym_id / _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 surface protein
B: Laminin-binding surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3164
Polymers59,1852
Non-polymers1312
Water1,36976
1
A: Laminin-binding surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6582
Polymers29,5931
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Laminin-binding surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6582
Polymers29,5931
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 93.990, 66.880
Angle α, β, γ (deg.)90.00, 105.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Laminin-binding surface protein


Mass: 29592.643 Da / Num. of mol.: 2 / Fragment: unp residues 32-306 / Mutation: delta(G123-L138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: ATCC BAA-611 / 2603 V/R / Gene: lmb, SAG1234 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8DZ80
#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.: 76 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 30% PEG2000 monomethyl ether 0.1 mM sodium citrate, 10 % ethylene glycol, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→32 Å / Num. all: 19430 / Num. obs: 19430 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
XRD1beamline home made softwaredata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HJT

3hjt


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 891 -RANDOM
Rwork0.24 ---
obs0.24 18265 92.3 %-
all-19430 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å2-8.53 Å2
2---4.59 Å20 Å2
3---1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 2 76 4242

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