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- PDB-7bnh: Complex structure at atomic resolution of SH3b domain with benzoi... -

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Basic information

Entry
Database: PDB / ID: 7bnh
TitleComplex structure at atomic resolution of SH3b domain with benzoic acid
ComponentsLysostaphin
KeywordsCELL ADHESION / CELL WALL TARGETING/BINDING / CWT / SH3 / COMPLEX / BENZOIC 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
BENZOIC ACID / lysostaphin
Similarity search - Component
Biological speciesStaphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 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 benzoic 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)22,57412
Polymers21,6382
Non-polymers93610
Water8,143452
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3457
Polymers10,8191
Non-polymers5256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2295
Polymers10,8191
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.954, 54.781, 51.490
Angle α, β, γ (deg.)90.000, 92.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 462 molecules

#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.37 %
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: 0.84→37.501 Å / Num. obs: 141746 / % possible obs: 83.7 % / Redundancy: 3.776 % / Biso Wilson estimate: 6.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.032 / Χ2: 0.954 / Net I/σ(I): 27.6 / Num. measured all: 535196
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
0.84-0.892.350.1325.31157802732267160.9680.16724.6
0.89-0.963.1960.0929.516580325636205920.9890.1180.3
0.96-1.033.7920.06315.68974423979236670.9950.07398.7
1.03-1.133.9320.03925.148465521989215290.9980.04697.9
1.13-1.264.0270.03332.047942519967197240.9980.03898.8
1.26-1.463.9350.0335.966731117575171040.9990.03597.3
1.46-1.794.1240.02743.416125414923148530.9990.03199.5
1.79-2.523.8370.02647.564274911533111420.9990.0396.6
2.52-37.5014.4360.02554.1928475646764190.9990.02899.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc6refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LEO

5leo


Resolution: 0.84→17.21 Å / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 9.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1012 2100 1.48 %
Rwork0.0852 139623 -
obs0.0854 141723 83.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.17 Å2 / Biso mean: 13.8033 Å2 / Biso min: 0.12 Å2
Refinement stepCycle: final / Resolution: 0.84→17.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 105 559 2196
Biso mean--14.15 21.42 -
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 (%)
0.84-0.860.1276170.15621125114210
0.86-0.880.1379500.14233341339130
0.88-0.910.1553880.12485822591053
0.91-0.930.12611320.11258831896380
0.93-0.960.10771660.1005110141118099
0.96-10.11741660.097110061117299
1-1.040.09711630.0895108481101198
1.04-1.090.09431620.0785107541091697
1.09-1.140.0871660.0718110581122499
1.14-1.220.08021660.0728110331119999
1.22-1.310.08861620.0774107921095497
1.31-1.440.09821640.0781108501101498
1.44-1.650.08451670.08041110911276100
1.65-2.080.10631660.0829110381120499
2.08-17.210.10981650.0894110021116797

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