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- PDB-4hx3: Crystal structure of Streptomyces caespitosus sermetstatin in com... -

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Basic information

Entry
Database: PDB / ID: 4hx3
TitleCrystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin
Components
  • Extracellular small neutral protease
  • Neutral proteinase inhibitor ScNPI
KeywordsHydrolase/Hydrolase Inhibitor / Streptomyces subtilisin inhibitor fold / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


snapalysin / serine-type endopeptidase inhibitor activity / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region / metal ion binding
Similarity search - Function
Peptidase M7, snapalysin / Streptomyces extracellular neutral proteinase (M7) family / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) ...Peptidase M7, snapalysin / Streptomyces extracellular neutral proteinase (M7) family / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular small neutral protease / Neutral proteinase inhibitor ScNPI
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_label_asym_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: Extracellular small neutral protease
B: Neutral proteinase inhibitor ScNPI
C: Extracellular small neutral protease
D: Neutral proteinase inhibitor ScNPI
E: Extracellular small neutral protease
F: Neutral proteinase inhibitor ScNPI
G: Extracellular small neutral protease
H: Neutral proteinase inhibitor ScNPI
I: Extracellular small neutral protease
J: Neutral proteinase inhibitor ScNPI
K: Extracellular small neutral protease
L: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,54620
Polymers158,97012
Non-polymers5778
Water4,954275
1
A: Extracellular small neutral protease
B: Neutral proteinase inhibitor ScNPI
C: Extracellular small neutral protease
D: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2137
Polymers52,9904
Non-polymers2233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-94 kcal/mol
Surface area20600 Å2
MethodPISA
2
E: Extracellular small neutral protease
F: Neutral proteinase inhibitor ScNPI
G: Extracellular small neutral protease
H: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1216
Polymers52,9904
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-96 kcal/mol
Surface area20400 Å2
MethodPISA
3
I: Extracellular small neutral protease
J: Neutral proteinase inhibitor ScNPI
K: Extracellular small neutral protease
L: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2137
Polymers52,9904
Non-polymers2233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-95 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.540, 121.810, 130.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer of dimer

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Components

#1: Protein
Extracellular small neutral protease / SCNP / Snapalysin


Mass: 14571.586 Da / Num. of mol.: 6 / Fragment: Mature protease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: snpA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56406, snapalysin
#2: Protein
Neutral proteinase inhibitor ScNPI / Sermetstatin


Mass: 11923.354 Da / Num. of mol.: 6
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→89.1 Å / Num. all: 51602 / Num. obs: 51602 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.19 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.7

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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 1KUH,4HWX

1kuh

4hwx


Resolution: 2.7→43.49 Å / Cor.coef. Fo:Fc: 0.9239 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.714 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 782 1.52 %RANDOM
Rwork0.195 ---
all0.195 51602 --
obs0.1957 51481 99.54 %-
Displacement parametersBiso mean: 57.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.4897 Å20 Å20 Å2
2---2.9934 Å20 Å2
3---4.4831 Å2
Refine analyzeLuzzati coordinate error obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11041 0 18 275 11334
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111352HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0615533HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes316HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1697HARMONIC5
X-RAY DIFFRACTIONt_it11352HARMONIC20
X-RAY DIFFRACTIONt_nbd15SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_chiral_improper_torsion1468SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12282SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2281 53 1.45 %
Rwork0.2263 3606 -
all0.2263 3659 -
obs--99.54 %
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)
11.3478-1.01651.23374.00540.92312.6585-0.05050.00650.137-0.0872-0.0515-0.3117-0.05720.32090.102-0.250.06280.0022-0.06790.0645-0.0036-23.7493-22.864224.2405
22.9744-0.02562.05383.24190.48644.1236-0.0110.23480.2318-0.6751-0.18270.3246-0.145-0.11020.1937-0.13350.1418-0.0766-0.0256-0.03360.045-48.0685-14.505710.1944
35.907-1.141-1.66487.4451.16624.78010.3792-0.00850.0748-0.1172-0.42390.83140.0341-0.69630.0447-0.24140.00340.04530.1398-0.10370.1294-70.6539-9.182931.4433
44.40090.94-0.59064.35410.98953.66980.2717-0.30170.7598-0.0270.0045-0.2457-0.64560.0405-0.2762-0.17960.0070.075-0.1503-0.04860.2346-43.68871.409426.6127
52.94390.9744-0.64937.9224-1.39645.1480.2222-0.5803-0.2335-0.1036-0.1962-1.62710.24680.9132-0.0259-0.15050.0314-0.04170.1414-0.00970.3922-5.2176-61.286717.4313
66.28062.84232.05425.0951.7713.66550.13530.12-0.62670.0336-0.0187-0.28150.34520.1775-0.1166-0.13530.05560.0151-0.1229-0.04940.037-30.3893-68.74093.5658
72.38790.2012-0.1056.05161.52044.257-0.1194-0.02790.0817-0.0725-0.31750.76250.0862-0.62380.4369-0.22840.06310.0208-0.0287-0.12020.0938-50.451-45.31146.8144
83.79211.9986-0.73964.16391.16942.2756-0.10250.45280.0313-0.67640.3226-0.3838-0.48840.1071-0.2201-0.0937-0.0040.1585-0.0379-0.03730.0511-23.8264-47.4263-3.6698
93.3211-0.78150.35161.5297-0.1944.0768-0.0282-0.0694-0.02690.18280.06420.10880.0301-0.3435-0.036-0.29240.05440.0107-0.10050.12880.0738-16.5261-40.785541.5487
104.3734-2.3132-0.76763.9104-0.26812.85050.1330.4473-0.0386-0.2966-0.0314-0.17680.3503-0.0867-0.1016-0.19870.0349-0.0389-0.1305-0.00270.19749.6321-53.711840.0417
113.43530.8591-0.64748.0101-0.07575.35740.0849-0.4257-0.36110.3999-0.8153-2.0587-0.42370.77520.7304-0.4647-0.1844-0.3032-0.27670.36370.829831.013-37.979156.4571
122.87030.8991-1.4432.8973-1.38893.73570.1085-0.3181-0.06450.4759-0.1144-0.4973-0.1684-0.02920.006-0.1729-0.0288-0.1584-0.120.02910.13824.8645-48.876463.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 132
2X-RAY DIFFRACTION1A201 - 999
3X-RAY DIFFRACTION2B1 - 113
4X-RAY DIFFRACTION3C-2 - 132
5X-RAY DIFFRACTION3C201 - 999
6X-RAY DIFFRACTION4D1 - 62
7X-RAY DIFFRACTION4D67 - 113
8X-RAY DIFFRACTION5E1 - 132
9X-RAY DIFFRACTION5E201 - 999
10X-RAY DIFFRACTION6F2 - 113
11X-RAY DIFFRACTION7G-1 - 132
12X-RAY DIFFRACTION7G201 - 999
13X-RAY DIFFRACTION8H-1 - 60
14X-RAY DIFFRACTION8H67 - 113
15X-RAY DIFFRACTION9I-2 - 132
16X-RAY DIFFRACTION9I201 - 999
17X-RAY DIFFRACTION10J1 - 65
18X-RAY DIFFRACTION10J68 - 113
19X-RAY DIFFRACTION11K-1 - 132
20X-RAY DIFFRACTION11K201 - 999
21X-RAY DIFFRACTION12L1 - 113

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