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- PDB-4hx2: Crystal structure of Streptomyces caespitosus sermetstatin in com... -

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Basic information

Entry
Database: PDB / ID: 4hx2
TitleCrystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin
Components
  • KerA
  • Neutral proteinase inhibitor ScNPI
KeywordsHydrolase/Hydrolase Inhibitor / Streptomyces subtilisin inhibitor fold / Subtilisin Carlsberg / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site ...Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R,2'R)-3,3'-oxydipropane-1,2-diol / ACETATE ION / CACODYLATE ION / ISOPROPYL ALCOHOL / : / PHOSPHATE ION / KerA / Neutral proteinase inhibitor ScNPI
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
Bacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTrillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X.
CitationJournal: CHEM SCI / Year: 2013
Title: Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes
Authors: Trillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: KerA
B: Neutral proteinase inhibitor ScNPI
C: KerA
D: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,68622
Polymers78,4594
Non-polymers1,22618
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.969, 83.624, 77.617
Angle α, β, γ (deg.)90.00, 110.78, 90.00
Int Tables number5
Space group name H-MC121
Detailsdimer of dimer

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein KerA / Subtilisin


Mass: 27306.199 Da / Num. of mol.: 2 / Fragment: Mature protease / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: Q9FDF2, subtilisin
#2: Protein Neutral proteinase inhibitor ScNPI / Sermetstatin


Mass: 11923.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: ScNPI / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: Q9FDS0

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Non-polymers , 11 types, 377 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-1AX / (2R,2'R)-3,3'-oxydipropane-1,2-diol


Mass: 166.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O5
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#12: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2010
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→48.6 Å / Num. all: 52346 / Num. obs: 52346 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.11 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SBC, 4HWX

1sbc

4hwx


Resolution: 2.25→32.94 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9143 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 797 1.52 %RANDOM
Rwork0.1767 ---
all0.177 52284 --
obs0.1772 52284 99.91 %-
Displacement parametersBiso mean: 51.65 Å2
Baniso -1Baniso -2Baniso -3
1-11.1322 Å20 Å29.5182 Å2
2---16.7826 Å20 Å2
3---5.6504 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: LAST / Resolution: 2.25→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5483 0 58 359 5900
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015630HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.127692HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes857HARMONIC5
X-RAY DIFFRACTIONt_it5630HARMONIC20
X-RAY DIFFRACTIONt_nbd13SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion2.52
X-RAY DIFFRACTIONt_chiral_improper_torsion773SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6525SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2602 52 1.36 %
Rwork0.2264 3765 -
all0.2268 3817 -
obs--99.91 %
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)
12.54280.50370.52571.4240.13123.07370.0244-0.0761-0.06240.001-0.070.0518-0.006-0.38710.0456-0.1476-0.0502-0.0207-0.01960.0031-0.1132-26.0192-23.6736-0.5288
23.4916-0.95552.60770.1656-0.55843.35030.1164-0.2356-0.1979-0.10280.07550.03590.1269-0.2419-0.1918-0.0804-0.0744-0.01960.07770.0028-0.0516-5.8921-22.161825.8442
33.38990.94160.50221.43180.00142.03330.1590.4665-0.8616-0.0481-0.098-0.13740.25430.1633-0.061-0.06780.0748-0.066-0.0538-0.20520.11541.08251.026233.5528
43.26440.54550.03681.67150.20691.3860.0286-0.33110.28920.14260.0709-0.0942-0.0821-0.1597-0.0995-0.0001-0.0253-0.08180.0057-0.07620.06638.5003-5.476835.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A302
4X-RAY DIFFRACTION2B-1 - 113
5X-RAY DIFFRACTION3C1 - 275
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION3C302
8X-RAY DIFFRACTION4D4 - 113

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