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- PDB-4m7g: Streptomyces Erythraeus Trypsin -

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Basic information

Entry
Database: PDB / ID: 4m7g
TitleStreptomyces Erythraeus Trypsin
ComponentsTrypsin-like protease
KeywordsHYDROLASE / Serine Protease
Function / homology
Function and homology information


chymotrypsin / trypsin / serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / Peptidase S1, PA clan, chymotrypsin-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain ...: / Peptidase S1, PA clan, chymotrypsin-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Trypsin / Chymotrypsin
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 Å
AuthorsBlankenship, E. / Vukoti, K. / Miyagi, M. / Lodowski, D.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state.
Authors: Blankenship, E. / Vukoti, K. / Miyagi, M. / Lodowski, D.T.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-like protease


Theoretical massNumber of molelcules
Total (without water)23,3411
Polymers23,3411
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.958, 61.249, 74.149
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 Trypsin-like protease


Mass: 23340.789 Da / Num. of mol.: 1 / Fragment: UNP residues 43-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Plasmid: PQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q54137, UniProt: P24664*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / pH: 7.9
Details: 10 mM calcium chloride, 100 mM HEPES pH 7.0, 2.72 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.688
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012
RadiationMonochromator: CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688 Å / Relative weight: 1
ReflectionResolution: 0.79→61.38 Å / Num. obs: 234158 / % possible obs: 99.8 %
Reflection shellResolution: 0.79→0.83 Å / Redundancy: 5.1 % / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata scaling
ARP/wARPmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SGT

1sgt


Resolution: 0.81→47.22 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.286 / SU ML: 0.008 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.12 11678 5 %RANDOM
Rwork0.109 ---
obs0.112 220874 99.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.81→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 353 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191959
X-RAY DIFFRACTIONr_bond_other_d0.0020.021829
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9542717
X-RAY DIFFRACTIONr_angle_other_deg3.09934221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12726.83579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.924154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212438
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0110.9471060
X-RAY DIFFRACTIONr_mcbond_other0.9420.9381059
X-RAY DIFFRACTIONr_mcangle_it1.2651.431367
X-RAY DIFFRACTIONr_mcangle_other1.5131324
X-RAY DIFFRACTIONr_scbond_it2.1311.184899
X-RAY DIFFRACTIONr_scbond_other1.709877
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0661.6011317
X-RAY DIFFRACTIONr_long_range_B_refined2.9839.1862528
X-RAY DIFFRACTIONr_long_range_B_other2.4468.3752289
X-RAY DIFFRACTIONr_rigid_bond_restr5.71231959
X-RAY DIFFRACTIONr_sphericity_free20.091550
X-RAY DIFFRACTIONr_sphericity_bonded9.89752194
LS refinement shellResolution: 0.81→0.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 874 -
Rwork0.341 15727 -
obs--96.86 %

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