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- PDB-4rkx: Identification and characterization of a small molecule inhibitor... -

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Basic information

Entry
Database: PDB / ID: 4rkx
TitleIdentification and characterization of a small molecule inhibitor of S. pyogenes SpeB.
ComponentsStreptopain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PAPAIN FOLD / CYSTEINE PROTEASE / SECRETED / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


streptopain / cysteine-type peptidase activity
Similarity search - Function
Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
benzyl (cyanomethyl)carbamate / NITRATE ION / Streptopain / :
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWang, A.Y. / Gonzalez-Paez, G.E. / Wolan, D.W.
CitationJournal: Biochemistry / Year: 2015
Title: Identification and Co-complex Structure of a New S. pyogenes SpeB Small Molecule Inhibitor.
Authors: Wang, A.Y. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 20, 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: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers28,6821
Non-polymers2522
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.564, 50.357, 37.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-796-

HOH

21A-797-

HOH

31A-798-

HOH

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Components

#1: Protein Streptopain /


Mass: 28681.693 Da / Num. of mol.: 1 / Fragment: UNP residues 146-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC 10782 / Gene: speB / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid
References: UniProt: E0PTS8, UniProt: A0A0M3KKW7*PLUS, streptopain
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-3S9 / benzyl (cyanomethyl)carbamate


Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M SODIUM NITRATE, 26% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. all: 26926 / Num. obs: 26926 / % possible obs: 89.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 13.87 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.089 / Net I/σ(I): 11
Reflection shellResolution: 1.59→1.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.65 / Num. unique all: 2327 / Rsym value: 0.26 / % possible all: 86.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8B

4d8b


Resolution: 1.59→31.32 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 1333 4.97 %Random
Rwork0.161 ---
obs0.1624 26810 89.53 %-
all-26810 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.59→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 18 206 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052023
X-RAY DIFFRACTIONf_angle_d0.9322747
X-RAY DIFFRACTIONf_dihedral_angle_d12.046721
X-RAY DIFFRACTIONf_chiral_restr0.04281
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.64680.25881280.20272426X-RAY DIFFRACTION87
1.6468-1.71280.24831240.19762572X-RAY DIFFRACTION91
1.7128-1.79070.20821390.17862592X-RAY DIFFRACTION92
1.7907-1.88510.19651380.16682566X-RAY DIFFRACTION92
1.8851-2.00320.21031250.15872600X-RAY DIFFRACTION92
2.0032-2.15780.17711320.1562562X-RAY DIFFRACTION90
2.1578-2.37490.19271370.15782554X-RAY DIFFRACTION90
2.3749-2.71840.21041380.16392550X-RAY DIFFRACTION89
2.7184-3.42420.18371470.162510X-RAY DIFFRACTION87
3.4242-31.32570.14971250.14722545X-RAY DIFFRACTION83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71940.69650.36113.36411.88821.5956-0.07110.03990.0236-0.06760.05760.0748-0.02940.04370.01970.09270.00210.00390.13220.03220.119721.8032-13.2603-16.2893
20.59421.16910.96773.39951.73662.1335-0.11730.00760.0062-0.04980.195-0.03920.00140.0933-0.10470.07470.01170.01310.10560.0220.082318.5183-14.94-14.8219
32.42911.5438-0.20612.89551.18961.87140.0134-0.3909-0.24650.3853-0.05630.3140.2934-0.11140.0680.17420.06080.04460.15280.07090.2096.8058-17.4194-5.8004
40.985-0.2155-0.67552.21132.81053.8344-0.16550.0679-0.1226-0.02520.07120.32950.00760.19660.16510.1491-0.0127-0.01160.14170.05180.22848.4089-26.6269-19.8672
52.74520.08090.88821.0874-0.08080.9964-0.0262-0.2762-0.24830.15420.08070.06530.0701-0.0515-0.04740.14360.02920.03690.11890.03560.119420.4747-17.9714-5.404
61.2184-0.9943-0.33432.02920.320.216-0.0269-0.0812-0.06060.00930.04260.25110.00250.0008-0.01090.0843-0.00110.00590.10490.03340.11735.9859-7.881-14.9935
71.993-0.3770.89023.26660.2822.78170.0030.040.23850.03620.1008-0.0492-0.1965-0.0529-0.11070.07550.00690.03370.09940.02120.12912.00284.4822-15.9498
82.6551-0.0516-0.68951.7224-0.48872.8053-0.04560.11240.0618-0.11970.0111-0.1352-0.02250.13530.02210.0982-0.00030.00370.07270.00830.096319.30570.6924-20.3824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 237 )
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 272 )
6X-RAY DIFFRACTION6chain 'A' and (resid 273 through 311 )
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 337 )
8X-RAY DIFFRACTION8chain 'A' and (resid 338 through 399 )

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