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- PDB-5ntb: Streptomyces papain inhibitor (SPI) -

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Basic information

Entry
Database: PDB / ID: 5ntb
TitleStreptomyces papain inhibitor (SPI)
ComponentsPapain inhibitor
KeywordsProtease inhibitor / Streptomyces papain inhibitor / transglutaminase / glutamine donor / Streptomyces mobaraensis
Function / homology
Function and homology information


negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
: / : / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / RlpA-like domain superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchmelz, S. / Juettner, N.E. / Fuchsbauer, H.L. / Scrima, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationVH-NG-727 Germany
CitationJournal: Protein Sci. / Year: 2018
Title: Illuminating structure and acyl donor sites of a physiological transglutaminase substrate from Streptomyces mobaraensis.
Authors: Juettner, N.E. / Schmelz, S. / Bogen, J.P. / Happel, D. / Fessner, W.D. / Pfeifer, F. / Fuchsbauer, H.L. / Scrima, A.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Papain inhibitor
B: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3725
Polymers24,0832
Non-polymers2883
Water4,179232
1
A: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2343
Polymers12,0421
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1382
Polymers12,0421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.350, 45.080, 112.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Papain inhibitor / SPI


Mass: 12041.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces mobaraensis (bacteria) / References: UniProt: P86242
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2.2M Ammonium sulphate, 200 mM Litium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.007 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.5→41.9 Å / Num. obs: 31262 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.6
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 12 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5375 / CC1/2: 0.789 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCW

4jcw


Resolution: 1.5→41.863 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.97
RfactorNum. reflection% reflection
Rfree0.1836 1563 5 %
Rwork0.1627 --
obs0.1638 31261 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 15 232 1921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061795
X-RAY DIFFRACTIONf_angle_d0.8972469
X-RAY DIFFRACTIONf_dihedral_angle_d9.831443
X-RAY DIFFRACTIONf_chiral_restr0.055272
X-RAY DIFFRACTIONf_plane_restr0.006322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.54850.24881380.21912632X-RAY DIFFRACTION100
1.5485-1.60380.26391390.20412647X-RAY DIFFRACTION100
1.6038-1.6680.21961410.18632666X-RAY DIFFRACTION100
1.668-1.7440.20771400.1742667X-RAY DIFFRACTION100
1.744-1.83590.21581400.17492652X-RAY DIFFRACTION100
1.8359-1.95090.20471420.15952711X-RAY DIFFRACTION100
1.9509-2.10150.17041410.15232665X-RAY DIFFRACTION100
2.1015-2.3130.17871410.1562688X-RAY DIFFRACTION100
2.313-2.64770.18731440.162743X-RAY DIFFRACTION100
2.6477-3.33560.19111440.16582737X-RAY DIFFRACTION100
3.3356-41.87920.15661530.15272890X-RAY DIFFRACTION100

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