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- PDB-4hwx: Crystal structure of Streptomyces caespitosus sermetstatin -

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Basic information

Entry
Database: PDB / ID: 4hwx
TitleCrystal structure of Streptomyces caespitosus sermetstatin
ComponentsNeutral proteinase inhibitor ScNPI
KeywordsHydrolase Inhibitor / Streptomyces subtilisin inhibitor fold
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Neutral proteinase inhibitor ScNPI
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1935
Polymers11,9231
Non-polymers2694
Water2,270126
1
A: Neutral proteinase inhibitor ScNPI
hetero molecules

A: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,38510
Polymers23,8472
Non-polymers5388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2970 Å2
ΔGint-17 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: Neutral proteinase inhibitor ScNPI
hetero molecules

A: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,38510
Polymers23,8472
Non-polymers5388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2310 Å2
ΔGint-18 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.040, 71.040, 52.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Neutral proteinase inhibitor ScNPI / Sermetstatin


Mass: 11923.354 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, 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: Oct 6, 2009
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→39.9 Å / Num. all: 12234 / Num. obs: 12234 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.43 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 40.3

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Processing

Software
NameVersionClassification
ProDCdata collection
SHELX& PHASERmodel building
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
SHELX& PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.89 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9258 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 479 3.92 %RANDOM
Rwork0.187 ---
all0.187 12232 --
obs0.1883 12232 99 %-
Displacement parametersBiso mean: 42.28 Å2
Baniso -1Baniso -2Baniso -3
1--5.4007 Å20 Å20 Å2
2---5.4007 Å20 Å2
3---10.8015 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 18 126 978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01870HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.141191HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d371SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes131HARMONIC5
X-RAY DIFFRACTIONt_it870HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion2.51
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact974SEMIHARMONIC4
LS refinement shellResolution: 1.9→2.08 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2207 479 3.73 %
Rwork0.2167 2762 -
all0.2168 2869 -
obs-12234 99 %
Refinement TLS params.Method: refined / Origin x: -3.4193 Å / Origin y: 25.3953 Å / Origin z: 2.1786 Å
111213212223313233
T0.0461 Å2-0.0491 Å2-0.0347 Å2-0.0134 Å20.0018 Å2---0.0396 Å2
L3.4644 °2-0.1265 °2-0.9308 °2-0.0427 °20.2121 °2--1.6503 °2
S0.1742 Å °0.1376 Å °-0.1384 Å °0.0224 Å °-0.1414 Å °-0.0492 Å °-0.0078 Å °-0.2086 Å °-0.0328 Å °
Refinement TLS groupSelection details: { A|* }

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