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- PDB-7bni: Complex structure of SH3b domain with 2-hydroxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 7bni
TitleComplex structure of SH3b domain with 2-hydroxybenzoic acid
ComponentsLysostaphin
KeywordsCELL ADHESION / CELL WALL TARGETING/BINDING / CWT / SH3 / COMPLEX / 2-hydroxybenzoic acid / Staphylococcus simulans
Function / homology
Function and homology information


lysostaphin / metallopeptidase activity
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / lysostaphin
Similarity search - Component
Biological speciesStaphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsMalecki, P.H. / Sabala, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-3D8D/16-00 Poland
CitationJournal: To Be Published
Title: Complex structure of SH3b domain with 2-hydroxybenzoic acid
Authors: Malecki, P.H. / Sabala, I.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysostaphin
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,75512
Polymers21,6382
Non-polymers1,11710
Water4,702261
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7029
Polymers10,8191
Non-polymers8838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0533
Polymers10,8191
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.719, 54.911, 49.181
Angle α, β, γ (deg.)90.000, 92.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysostaphin


Mass: 10819.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus simulans (bacteria) / Gene: HMPREF3215_01322 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A133QQ41, lysostaphin
#2: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% PEG 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.31→36.684 Å / Num. obs: 46043 / % possible obs: 97.4 % / Redundancy: 4.953 % / Biso Wilson estimate: 20.774 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 0.916 / Net I/σ(I): 15.18 / Num. measured all: 228042
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.31-1.394.720.7971.834087756372220.6930.89795.5
1.39-1.484.9570.542.8134795718670200.8430.60597.7
1.48-1.64.740.2974.9230518666564380.9440.33496.6
1.6-1.755.1910.1688.9231551612260780.9810.18799.3
1.75-1.965.1070.08715.827982557254790.9940.09798.3
1.96-2.264.7180.04924.8622282489347230.9980.05596.5
2.26-2.775.2860.03634.721731416741110.9990.0498.7
2.77-3.94.9720.03144.715807325131790.9980.03597.8
3.9-36.6845.1810.02951.159289184117930.9990.03297.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LEO

5leo


Resolution: 1.31→18.81 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1797 2099 4.56 %
Rwork0.1459 43933 -
obs0.1474 46032 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.91 Å2 / Biso mean: 21.2445 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.31→18.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 73 278 1883
Biso mean--32.48 35.76 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.340.24751290.23462718284792
1.34-1.370.29261410.21432944308598
1.37-1.410.23511420.19712961310398
1.41-1.450.25821380.18672891302998
1.45-1.50.24721390.17072918305797
1.5-1.550.19291350.16212827296295
1.55-1.610.20491420.14492963310598
1.61-1.680.1771420.13952970311299
1.69-1.770.19171430.13212989313299
1.77-1.880.16621420.12982973311599
1.88-2.030.15481400.12532925306597
2.03-2.230.15961370.1282884302196
2.23-2.560.15961430.13932974311799
2.56-3.220.18921420.13992990313299
3.22-18.810.16581440.14883006315097

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